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Strontium in PDB 6van: Crystal Structure of Caltubin From the Great Pond Snail

Protein crystallography data

The structure of Crystal Structure of Caltubin From the Great Pond Snail, PDB code: 6van was solved by A.Dong, A.Li, Q.Zhang, A.Barszczyk, Y.H.Chern, C.H.Arrowsmith, A.M.Edwards, Z.P.Zhong, Y.Tong, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 1.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.026, 32.632, 85.955, 90.00, 105.19, 90.00
R / Rfree (%) 19.1 / 22.2

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Strontium atom in the Crystal Structure of Caltubin From the Great Pond Snail (pdb code 6van). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 17 binding sites of Strontium where determined in the Crystal Structure of Caltubin From the Great Pond Snail, PDB code: 6van:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 17 in 6van

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Strontium binding site 1 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:19.5
occ:0.70
SR A:SR201 0.0 19.5 0.7
SR A:SR201 1.2 13.8 0.3
O A:GLN58 2.4 19.5 1.0
OD2 A:ASP56 2.5 24.1 1.0
OE2 A:GLU63 2.6 24.6 1.0
OE1 A:GLU63 2.6 23.3 1.0
OD1 A:ASP52 2.6 24.1 1.0
O A:HOH399 2.6 32.1 1.0
UNK A:UNX210 2.7 30.0 1.0
OD1 A:ASP56 2.7 25.3 1.0
CD A:GLU63 2.9 22.6 1.0
CG A:ASP56 2.9 25.2 1.0
C A:GLN58 3.6 21.7 1.0
CG A:ASP52 3.7 24.5 1.0
CG A:GLU63 4.4 23.9 1.0
CB A:ASP56 4.4 24.8 1.0
CB A:ASP52 4.4 23.6 1.0
CA A:GLN58 4.4 23.3 1.0
N A:SER59 4.5 19.9 1.0
OD2 A:ASP52 4.5 23.1 1.0
N A:GLN58 4.5 24.0 1.0
CA A:ASP52 4.5 23.4 1.0
CA A:SER59 4.6 21.1 1.0
CB A:GLN58 4.6 25.4 1.0
N A:THR60 4.6 23.4 1.0
OG1 A:THR60 4.7 25.6 1.0
CG2 A:THR60 4.8 23.7 1.0
N A:ASP56 4.9 23.9 1.0
CB A:ASP54 4.9 24.4 1.0
OD2 A:ASP54 4.9 25.7 1.0

Strontium binding site 2 out of 17 in 6van

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Strontium binding site 2 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:13.8
occ:0.30
SR A:SR201 0.0 13.8 0.3
SR A:SR201 1.2 19.5 0.7
OD1 A:ASP52 2.0 24.1 1.0
OE2 A:GLU63 2.4 24.6 1.0
OD2 A:ASP56 2.5 24.1 1.0
UNK A:UNX210 2.9 30.0 1.0
O A:GLN58 3.1 19.5 1.0
CG A:ASP56 3.2 25.2 1.0
CD A:GLU63 3.2 22.6 1.0
OD1 A:ASP56 3.3 25.3 1.0
CG A:ASP52 3.3 24.5 1.0
OE1 A:GLU63 3.4 23.3 1.0
O A:HOH399 3.7 32.1 1.0
CB A:ASP54 3.8 24.4 1.0
CA A:ASP52 3.9 23.4 1.0
OD2 A:ASP54 4.0 25.7 1.0
CB A:ASP52 4.0 23.6 1.0
N A:ASP54 4.1 24.0 1.0
C A:ASP52 4.2 25.0 1.0
OD2 A:ASP52 4.2 23.1 1.0
C A:GLN58 4.4 21.7 1.0
CG A:ASP54 4.4 24.1 1.0
CA A:ASP54 4.4 24.7 1.0
N A:ASP56 4.4 23.9 1.0
N A:HIS53 4.4 26.2 1.0
CB A:ASP56 4.4 24.8 1.0
CG A:GLU63 4.5 23.9 1.0
O A:HOH346 4.6 25.5 1.0
N A:ASN55 4.6 24.8 1.0
O A:ASP52 4.7 25.4 1.0
C A:ASP54 4.7 25.9 1.0

Strontium binding site 3 out of 17 in 6van

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Strontium binding site 3 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr202

b:25.3
occ:1.00
OD1 A:ASN92 2.3 18.6 1.0
OD2 A:ASP96 2.3 17.1 1.0
O A:ALA94 2.4 16.8 1.0
OD1 A:ASP88 2.4 19.7 1.0
OD1 A:ASN90 2.4 18.1 1.0
OE1 A:GLU100 2.4 15.4 1.0
OE2 A:GLU100 2.5 17.3 1.0
CD A:GLU100 2.7 17.1 1.0
CG A:ASN92 3.2 21.4 1.0
CG A:ASN90 3.3 18.5 1.0
CG A:ASP96 3.5 16.5 1.0
CG A:ASP88 3.5 18.8 1.0
C A:ALA94 3.6 17.1 1.0
ND2 A:ASN90 3.6 17.5 1.0
ND2 A:ASN92 3.8 22.3 1.0
CA A:ASP88 3.9 18.6 1.0
CB A:ASP88 4.1 18.6 1.0
N A:ASP96 4.1 15.4 1.0
N A:ASN92 4.2 22.6 1.0
N A:ALA94 4.2 19.0 1.0
CG A:GLU100 4.2 16.6 1.0
CB A:ASP96 4.3 16.7 1.0
OD1 A:ASP96 4.3 20.2 1.0
OD2 A:ASP88 4.4 22.0 1.0
C A:ASP88 4.4 19.9 1.0
CB A:ASN92 4.4 22.2 1.0
CA A:ALA94 4.4 18.8 1.0
N A:ASN90 4.4 21.1 1.0
N A:ILE95 4.5 17.1 1.0
CA A:ILE95 4.5 16.5 1.0
N A:GLY91 4.5 22.6 1.0
CB A:ASN90 4.6 19.2 1.0
C A:ILE95 4.7 15.7 1.0
CA A:ASN92 4.7 23.1 1.0
N A:SER89 4.7 20.0 1.0
CA A:ASN90 4.8 20.1 1.0
N A:GLY93 4.8 24.0 1.0
C A:ASN90 4.8 21.9 1.0
CB A:ALA94 4.9 21.4 1.0
CA A:ASP96 4.9 16.1 1.0
O A:ASP88 4.9 22.9 1.0
C A:ASN92 4.9 23.8 1.0

Strontium binding site 4 out of 17 in 6van

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Strontium binding site 4 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr203

b:15.7
occ:1.00
OD1 A:ASN125 2.4 14.5 1.0
OD1 A:ASP123 2.4 12.2 1.0
O A:PHE129 2.4 12.8 1.0
OD1 A:ASP127 2.4 14.7 1.0
O A:HOH364 2.5 17.8 1.0
OE2 A:GLU134 2.5 12.9 1.0
OE1 A:GLU134 2.5 12.4 1.0
CD A:GLU134 2.9 11.5 1.0
CG A:ASP127 3.3 15.4 1.0
CG A:ASN125 3.5 14.9 1.0
CG A:ASP123 3.5 12.0 1.0
C A:PHE129 3.6 11.6 1.0
OD2 A:ASP127 3.8 16.9 1.0
ND2 A:ASN125 4.1 16.3 1.0
CA A:ASP123 4.2 11.2 1.0
N A:ASP127 4.2 14.6 1.0
N A:ASN125 4.3 13.7 1.0
N A:PHE129 4.3 12.3 1.0
C A:ASP123 4.3 12.3 1.0
OD2 A:ASP123 4.4 14.0 1.0
CB A:ASP123 4.4 11.9 1.0
CG A:GLU134 4.4 11.1 1.0
N A:THR124 4.4 12.2 1.0
CB A:ASP127 4.4 15.4 1.0
CA A:PHE129 4.4 12.8 1.0
N A:VAL130 4.5 11.1 1.0
CA A:VAL130 4.5 11.1 1.0
CB A:ASN125 4.6 14.5 1.0
N A:ASP126 4.6 14.2 1.0
O A:HOH413 4.6 29.9 1.0
O A:HOH315 4.7 19.3 1.0
CB A:PHE129 4.7 13.8 1.0
N A:THR131 4.7 10.7 1.0
CA A:ASP127 4.7 14.5 1.0
CA A:ASN125 4.8 14.2 1.0
CG2 A:THR131 4.8 12.9 1.0
C A:ASN125 4.8 14.8 1.0
N A:SER128 4.9 14.1 1.0
O A:ASP123 5.0 12.3 1.0
C A:ASP127 5.0 14.2 1.0

Strontium binding site 5 out of 17 in 6van

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Strontium binding site 5 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr204

b:14.8
occ:1.00
OD1 A:ASN163 2.4 17.6 1.0
O A:LYS167 2.5 12.2 1.0
OD1 A:ASP161 2.5 11.5 1.0
OD1 A:ASP165 2.5 14.5 1.0
O A:HOH313 2.5 24.0 1.0
OE1 A:GLU172 2.6 13.1 1.0
OE2 A:GLU172 2.7 13.1 1.0
O A:HOH381 2.9 27.7 1.0
CD A:GLU172 3.0 11.5 1.0
CG A:ASP165 3.3 16.1 1.0
CG A:ASN163 3.5 20.8 1.0
CG A:ASP161 3.6 12.0 1.0
OD2 A:ASP165 3.7 18.9 1.0
C A:LYS167 3.7 12.0 1.0
ND2 A:ASN163 4.0 22.7 1.0
CA A:ASP161 4.3 11.7 1.0
OD2 A:ASP161 4.4 13.6 1.0
N A:ASP165 4.4 15.5 1.0
CA A:LEU168 4.4 10.1 1.0
CB A:ASP161 4.4 11.8 1.0
N A:ASN163 4.5 15.5 1.0
N A:LEU168 4.5 10.1 1.0
CG A:GLU172 4.5 11.2 1.0
N A:LYS167 4.5 12.9 1.0
C A:ASP161 4.6 12.4 1.0
N A:ALA162 4.6 13.2 1.0
CB A:ASP165 4.6 15.7 1.0
O A:HOH365 4.7 27.7 1.0
CG A:LYS167 4.7 14.6 1.0
CA A:LYS167 4.7 12.7 1.0
N A:SER169 4.7 10.5 1.0
CB A:ASN163 4.7 19.1 1.0
N A:LYS164 4.8 16.0 0.5
O A:HOH417 4.8 29.4 1.0
CA A:ASP165 4.9 15.4 1.0
N A:LYS164 4.9 15.7 0.5
CA A:ASN163 5.0 17.3 1.0
C A:LEU168 5.0 9.3 1.0

Strontium binding site 6 out of 17 in 6van

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Strontium binding site 6 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr205

b:42.5
occ:1.00
O A:HOH317 2.7 38.5 1.0
O A:HOH412 2.9 41.3 1.0
OG1 A:THR79 3.1 23.6 1.0
N A:THR76 3.4 17.5 1.0
OG1 A:THR76 3.6 20.4 1.0
CB A:THR79 3.6 20.3 1.0
NZ A:LYS72 3.7 21.5 1.0
CE A:LYS72 3.7 20.6 1.0
CA A:VAL75 3.8 18.7 1.0
CG2 A:VAL75 3.8 18.9 1.0
CG2 A:THR76 3.9 20.2 1.0
CG2 A:THR79 4.1 20.7 1.0
C A:VAL75 4.1 18.4 1.0
CD A:LYS72 4.1 18.8 1.0
CB A:THR76 4.1 19.1 1.0
O A:HOH339 4.2 18.5 0.5
O A:HOH339 4.3 23.1 0.5
CB A:VAL75 4.3 18.6 1.0
CA A:THR76 4.3 19.4 1.0
O A:ASP74 4.6 20.6 0.5
OD1 A:ASP126 4.7 22.6 1.0
N A:VAL75 4.9 17.6 1.0
O A:ASP74 4.9 18.9 0.5
O A:THR76 4.9 19.4 1.0
OD2 A:ASP126 5.0 22.3 1.0

Strontium binding site 7 out of 17 in 6van

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Strontium binding site 7 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr206

b:65.7
occ:1.00
O A:HOH372 2.6 23.3 1.0
O A:HOH359 2.6 30.7 1.0
O A:GLN154 2.8 17.4 1.0
C A:GLN154 3.9 13.4 1.0
CA A:GLY155 4.5 13.2 1.0
N A:GLY155 4.6 12.6 1.0
O A:GLY155 4.7 15.4 1.0
CA A:GLN154 4.9 12.5 1.0
CB A:GLN154 5.0 13.6 1.0

Strontium binding site 8 out of 17 in 6van

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Strontium binding site 8 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr207

b:22.0
occ:1.00
O A:HOH382 2.4 34.8 1.0
O A:SER178 2.4 17.2 1.0
O A:HOH345 2.5 21.1 1.0
O A:HOH404 2.6 40.2 1.0
OG A:SER178 2.6 17.1 1.0
O A:HOH375 2.9 31.4 1.0
CB A:SER178 3.4 15.4 1.0
C A:SER178 3.5 16.5 1.0
CA A:SER178 4.1 15.2 1.0
N A:PRO179 4.6 16.8 1.0
O A:THR175 4.6 13.2 1.0
O A:HOH388 4.9 23.8 1.0
CA A:PRO179 4.9 18.4 1.0
N A:SER178 4.9 13.3 1.0
O1 A:EDO209 5.0 24.8 1.0

Strontium binding site 9 out of 17 in 6van

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Strontium binding site 9 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr208

b:37.6
occ:1.00
O A:HOH377 2.6 34.3 1.0
OD1 A:ASP54 4.5 26.0 1.0

Strontium binding site 10 out of 17 in 6van

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Strontium binding site 10 out of 17 in the Crystal Structure of Caltubin From the Great Pond Snail


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structure of Caltubin From the Great Pond Snail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:12.7
occ:1.00
O B:GLN58 2.5 12.3 0.7
OD1 B:ASP52 2.5 12.6 1.0
O B:GLN58 2.6 10.6 0.3
OE2 B:GLU63 2.6 12.7 1.0
OD1 B:ASP56 2.6 14.9 1.0
OD1 B:ASP54 2.7 19.2 1.0
O2 B:EDO209 2.7 17.4 1.0
O1 B:EDO209 2.7 18.9 1.0
OE1 B:GLU63 2.8 12.6 1.0
OD2 B:ASP54 2.9 22.7 1.0
CD B:GLU63 3.0 11.4 1.0
CG B:ASP54 3.2 16.4 1.0
CG B:ASP56 3.4 15.2 1.0
C1 B:EDO209 3.5 21.6 1.0
C2 B:EDO209 3.6 20.2 1.0
CG B:ASP52 3.6 11.9 1.0
C B:GLN58 3.8 10.7 0.3
C B:GLN58 3.8 12.3 0.7
OD2 B:ASP56 3.8 19.8 1.0
CB B:ASP52 4.3 11.2 1.0
CA B:ASP52 4.3 10.4 1.0
OD2 B:ASP52 4.4 13.2 1.0
CB B:ASP56 4.5 14.6 1.0
CG B:GLU63 4.5 11.2 1.0
N B:GLN58 4.6 11.6 0.3
CA B:GLN58 4.6 11.0 0.3
N B:GLN58 4.6 13.2 0.7
O B:HOH362 4.6 25.2 1.0
N B:ASP56 4.6 11.7 1.0
CB B:GLN58 4.7 11.0 0.3
CB B:ASP54 4.7 14.0 1.0
N B:SER59 4.7 10.5 1.0
CA B:GLN58 4.7 13.6 0.7
CA B:SER59 4.8 10.1 1.0
C B:ASP52 4.8 11.2 1.0
CG B:GLN58 4.8 18.8 0.7
O B:HOH388 4.9 34.7 1.0
O B:HOH389 5.0 38.2 1.0
O B:LEU51 5.0 10.7 1.0

Reference:

A.Dong, A.Li, Q.Zhang, A.Barszczyk, Y.H.Chern, C.H.Arrowsmith, A.M.Edwards, Z.P.Zhong, Y.Tong, Structural Genomics Consortium (Sgc). Cell-Penetrating Caltubin Promotes Neurite Outgrowth and Regrowth Through Calcium-Dependent Microtubule Regulation To Be Published.
Page generated: Mon Jan 25 16:04:27 2021

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