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Strontium in PDB 2spt: Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1

Enzymatic activity of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1

All present enzymatic activity of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1:
3.4.21.5;

Protein crystallography data

The structure of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1, PDB code: 2spt was solved by A.Tulinsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.690, 54.120, 131.170, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Strontium Binding Sites:

The binding sites of Strontium atom in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 (pdb code 2spt). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 8 binding sites of Strontium where determined in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1, PDB code: 2spt:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Strontium binding site 1 out of 8 in 2spt

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Strontium binding site 1 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr171

b:35.2
occ:1.00
 OE11 A:CGU30 2.2 34.2 1.0
OE21 A:CGU30 2.6 36.4 1.0
OE12 A:CGU26 2.7 37.5 1.0
OE21 A:CGU26 2.7 36.9 1.0
CD1 A:CGU30 3.3 34.0 1.0
CD1 A:CGU26 3.5 37.2 1.0
CD2 A:CGU30 3.6 35.0 1.0
CD2 A:CGU26 3.7 37.6 1.0
CG A:CGU30 3.8 34.4 1.0
OE11 A:CGU26 4.2 37.8 1.0
CG A:CGU26 4.3 36.8 1.0
OE12 A:CGU30 4.4 33.5 1.0
OE22 A:CGU30 4.7 37.0 1.0
SR A:SR172 4.8 42.5 1.0
OE22 A:CGU26 4.8 39.2 1.0
O A:CGU26 4.9 32.1 1.0

Strontium binding site 2 out of 8 in 2spt

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Strontium binding site 2 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr172

b:42.5
occ:1.00
 OE21 A:CGU30 2.6 36.4 1.0
OE22 A:CGU30 2.7 37.0 1.0
OE12 A:CGU27 2.9 37.6 1.0
CD2 A:CGU30 3.1 35.0 1.0
OE12 A:CGU8 3.5 46.4 1.0
CD1 A:CGU8 3.6 46.0 1.0
OE11 A:CGU27 3.7 37.8 1.0
CD1 A:CGU27 3.7 36.3 1.0
O A:HOH191 3.8 43.5 1.0
OE11 A:CGU8 3.9 45.2 1.0
CG A:CGU8 4.1 45.7 1.0
SR A:SR173 4.2 41.4 1.0
CG A:CGU30 4.6 34.4 1.0
OE21 A:CGU26 4.6 36.9 1.0
ND2 A:ASN2 4.7 44.1 1.0
SR A:SR171 4.8 35.2 1.0
CB A:CGU8 4.8 44.0 1.0
O A:CGU26 4.9 32.1 1.0
OE12 A:CGU26 4.9 37.5 1.0
CD2 A:CGU26 4.9 37.6 1.0
OD1 A:ASN2 5.0 42.5 1.0

Strontium binding site 3 out of 8 in 2spt

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Strontium binding site 3 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


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Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr173

b:41.4
occ:1.00
 OE11 A:CGU17 2.7 40.1 1.0
OE22 A:CGU30 2.8 37.0 1.0
OE11 A:CGU27 3.0 37.8 1.0
CD1 A:CGU17 3.2 39.4 1.0
OE12 A:CGU17 3.2 39.8 1.0
OE11 A:CGU8 3.9 45.2 1.0
CD2 A:CGU30 4.0 35.0 1.0
CD1 A:CGU27 4.1 36.3 1.0
CB A:CGU30 4.1 33.5 1.0
SR A:SR174 4.1 43.6 1.0
SR A:SR172 4.2 42.5 1.0
CG A:CGU17 4.5 38.6 1.0
CA A:GLY12 4.6 33.7 1.0
CG A:CGU30 4.6 34.4 1.0
OE12 A:CGU27 4.7 37.6 1.0
OE21 A:CGU30 4.8 36.4 1.0
O A:CGU27 4.8 32.9 1.0
CD1 A:CGU8 4.8 46.0 1.0
CA A:CGU27 4.9 32.9 1.0
O A:ARG10 4.9 38.4 1.0
CD2 A:CGU17 5.0 39.6 1.0

Strontium binding site 4 out of 8 in 2spt

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Strontium binding site 4 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr174

b:43.6
occ:1.00
 OE21 A:CGU17 2.2 39.8 1.0
OE11 A:CGU27 2.7 37.8 1.0
OE22 A:CGU27 2.7 35.9 1.0
CD2 A:CGU17 2.8 39.6 1.0
OD1 A:ASN2 3.0 42.5 1.0
N A:ALA1 3.1 45.4 1.0
OE11 A:CGU7 3.2 41.1 1.0
OE11 A:CGU17 3.3 40.1 1.0
CG A:CGU17 3.4 38.6 1.0
N A:ASN2 3.4 45.2 1.0
CD1 A:CGU27 3.5 36.3 1.0
OE22 A:CGU17 3.6 40.7 1.0
CD1 A:CGU17 3.6 39.4 1.0
OE11 A:CGU8 3.6 45.2 1.0
CD1 A:CGU7 3.8 41.1 1.0
CD2 A:CGU27 3.9 34.5 1.0
CG A:ASN2 4.0 44.0 1.0
SR A:SR175 4.1 39.1 1.0
SR A:SR173 4.1 41.4 1.0
C A:ALA1 4.1 45.9 1.0
CA A:ALA1 4.2 45.6 1.0
CA A:ASN2 4.2 44.8 1.0
CG A:CGU27 4.2 35.1 1.0
O A:HOH181 4.2 20.9 0.7
OE12 A:CGU27 4.3 37.6 1.0
OE12 A:CGU7 4.4 39.2 1.0
CD1 A:CGU8 4.5 46.0 1.0
OE12 A:CGU8 4.6 46.4 1.0
OE12 A:CGU17 4.7 39.8 1.0
CG A:CGU7 4.7 41.8 1.0
CB A:ASN2 4.7 44.3 1.0
OE21 A:CGU27 4.8 33.8 1.0
CB A:CGU27 4.8 33.7 1.0
CB A:CGU17 4.8 36.0 1.0
ND2 A:ASN2 4.8 44.1 1.0

Strontium binding site 5 out of 8 in 2spt

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Strontium binding site 5 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr175

b:39.1
occ:1.00
 OE21 A:CGU17 2.6 39.8 1.0
OE11 A:CGU7 2.7 41.1 1.0
OE22 A:CGU21 2.7 37.7 1.0
OE12 A:CGU7 2.9 39.2 1.0
CD1 A:CGU7 3.1 41.1 1.0
N A:ALA1 3.1 45.4 1.0
OE21 A:CGU21 3.2 39.3 1.0
CD2 A:CGU21 3.4 37.6 1.0
CD2 A:CGU17 3.4 39.6 1.0
OE22 A:CGU17 3.5 40.7 1.0
N A:ASN2 3.9 45.2 1.0
CA A:ALA1 4.1 45.6 1.0
SR A:SR174 4.1 43.6 1.0
CB A:ALA1 4.1 45.4 1.0
C A:ALA1 4.4 45.9 1.0
O A:HOH181 4.5 20.9 0.7
N A:LYS3 4.6 44.9 1.0
CG A:CGU7 4.7 41.8 1.0
CG A:CGU21 4.8 37.4 1.0
CA A:ASN2 4.9 44.8 1.0
CG A:CGU17 4.9 38.6 1.0

Strontium binding site 6 out of 8 in 2spt

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Strontium binding site 6 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr176

b:37.4
occ:0.66
 OE21 A:CGU21 2.3 39.3 1.0
OE11 A:CGU21 2.9 37.9 1.0
OE12 A:CGU20 2.9 36.6 1.0
CD2 A:CGU21 3.3 37.6 1.0
CD1 A:CGU21 3.6 37.7 1.0
CG A:CGU21 3.8 37.4 1.0
CD1 A:CGU20 3.9 36.1 1.0
OE22 A:CGU21 4.4 37.7 1.0
OE11 A:CGU20 4.5 35.7 1.0
OE12 A:CGU21 4.6 38.1 1.0
CG A:CGU20 4.9 35.2 1.0
O A:ARG16 4.9 32.3 1.0

Strontium binding site 7 out of 8 in 2spt

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Strontium binding site 7 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr177

b:34.2
occ:0.63
 OE21 A:CGU20 2.4 34.5 1.0
OE22 A:CGU15 2.8 33.6 1.0
OE22 A:CGU20 3.1 33.8 1.0
CD2 A:CGU20 3.1 34.7 1.0
CD2 A:CGU15 3.7 33.8 1.0
OE21 A:CGU15 4.1 32.6 1.0
CG A:CGU20 4.6 35.2 1.0
NH1 A:ARG55 4.7 47.7 1.0
OE11 A:CGU20 4.7 35.7 1.0
CG A:CGU15 4.8 35.1 1.0
NH2 A:ARG55 4.9 48.1 1.0

Strontium binding site 8 out of 8 in 2spt

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Strontium binding site 8 out of 8 in the Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Differences in the Metal Ion Structure Between Sr-and Ca-Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr178

b:33.8
occ:0.43
 O A:HOH199 2.2 25.1 0.9
OE12 A:CGU30 3.0 33.5 1.0
O A:CGU30 3.1 34.1 1.0
C A:CGU30 3.9 33.6 1.0
CA A:CGU30 4.0 33.3 1.0
CB A:CGU30 4.2 33.5 1.0
CD1 A:CGU30 4.2 34.0 1.0
CG A:CGU30 4.9 34.4 1.0
N A:GLY12 5.0 35.2 1.0

Reference:

T.P.Seshadri, E.Skrzypczak-Jankun, M.Yin, A.Tulinsky. Differences in the Metal Ion Structure Between Sr- and Ca-Prothrombin Fragment 1. Biochemistry V. 33 1087 1994.
ISSN: ISSN 0006-2960
PubMed: 8110739
DOI: 10.1021/BI00171A006
Page generated: Thu Oct 10 21:27:15 2024

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