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Calcium in PDB 3vv3: Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913

Protein crystallography data

The structure of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913, PDB code: 3vv3 was solved by G.Y.Zhao, X.Gao, X.L.Chen, Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.40 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.792, 72.454, 137.627, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 (pdb code 3vv3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913, PDB code: 3vv3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3vv3

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Calcium binding site 1 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:30.0
occ:1.00
 OE2 A:GLU69 2.3 6.7 1.0
OD1 A:ASP85 2.3 4.1 1.0
O A:TYR82 2.4 6.5 1.0
OD1 A:ASP78 2.4 5.8 1.0
OD1 A:ASP76 2.4 4.7 1.0
OD1 A:ASN80 2.5 4.0 1.0
CD A:GLU69 3.3 9.8 1.0
CG A:ASP85 3.4 10.4 1.0
CG A:ASP76 3.5 11.4 1.0
CG A:ASP78 3.5 11.1 1.0
CG A:ASN80 3.5 9.4 1.0
C A:TYR82 3.5 8.8 1.0
CG A:GLU69 3.6 9.3 1.0
OD2 A:ASP78 3.9 11.4 1.0
OD2 A:ASP85 3.9 5.6 1.0
CA A:ASP76 4.0 6.8 1.0
ND2 A:ASN80 4.0 5.9 1.0
CB A:ASP76 4.2 7.6 1.0
N A:TYR82 4.3 5.2 1.0
C A:ASP76 4.3 7.3 1.0
OD2 A:ASP76 4.3 7.8 1.0
CA A:TYR82 4.4 6.4 1.0
N A:ASN80 4.4 6.1 1.0
OE1 A:GLU69 4.4 4.8 1.0
N A:ASP78 4.4 6.1 1.0
N A:ASN77 4.4 5.2 1.0
N A:ASP85 4.4 6.6 1.0
N A:ASP84 4.5 6.1 1.0
N A:ILE83 4.5 7.2 1.0
CB A:ASP85 4.5 5.8 1.0
ND2 A:ASN66 4.6 5.0 1.0
CA A:ILE83 4.6 5.8 1.0
CB A:TYR82 4.7 6.5 1.0
CB A:ASN80 4.7 10.1 1.0
N A:GLY79 4.7 6.9 1.0
CB A:ASP78 4.7 8.9 1.0
C A:ILE83 4.8 8.9 1.0
O A:ASP76 4.9 8.7 1.0
CA A:ASN80 4.9 7.2 1.0
CA A:ASP78 4.9 9.3 1.0
N A:GLY81 5.0 9.4 1.0

Calcium binding site 2 out of 8 in 3vv3

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Calcium binding site 2 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:30.0
occ:1.00
 OD1 A:ASP25 2.3 8.9 1.0
O A:HOH522 2.3 8.6 1.0
O A:HOH509 2.3 5.6 1.0
OD1 A:ASP29 2.5 7.1 1.0
OD2 A:ASP27 2.6 8.4 1.0
O A:HOH532 2.6 8.1 1.0
OD1 A:ASP27 2.6 6.2 1.0
CG A:ASP27 2.9 7.6 1.0
CG A:ASP25 3.5 8.8 1.0
CG A:ASP29 3.8 7.9 1.0
CA A:CA403 3.8 30.0 1.0
CA A:ASP25 3.9 8.9 1.0
O A:HOH614 3.9 12.5 1.0
O A:HOH544 4.2 9.3 1.0
CB A:ASP25 4.2 8.9 1.0
ND2 A:ASN15 4.2 6.5 1.0
O A:HOH785 4.3 26.1 1.0
CA A:ASP29 4.3 7.0 1.0
OE2 A:GLU32 4.3 13.0 1.0
OD2 A:ASP25 4.5 6.1 1.0
CB A:ASP27 4.5 5.9 1.0
OE1 A:GLU32 4.5 10.2 1.0
O A:ASP25 4.5 9.9 1.0
C A:ASP25 4.6 8.3 1.0
O A:HOH883 4.6 35.9 1.0
N A:ASP29 4.6 6.6 1.0
OD2 A:ASP29 4.6 5.9 1.0
CB A:ASP29 4.7 7.5 1.0
O A:ASN16 4.7 9.5 1.0
CD A:GLU32 4.7 16.2 1.0
N A:ASP25 4.8 9.2 1.0
N A:ASN16 4.9 9.4 1.0

Calcium binding site 3 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 3 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:30.0
occ:1.00
 O A:HOH614 2.2 12.5 1.0
OD2 A:ASP29 2.5 5.9 1.0
O A:HOH643 2.5 20.4 1.0
OD1 A:ASP25 2.5 8.9 1.0
OD2 A:ASP25 2.5 6.1 1.0
O A:HOH615 2.5 16.1 1.0
OD1 A:ASP29 2.6 7.1 1.0
O A:HOH544 2.7 9.3 1.0
CG A:ASP25 2.8 8.8 1.0
CG A:ASP29 2.9 7.9 1.0
CA A:CA402 3.8 30.0 1.0
O A:HOH509 4.2 5.6 1.0
CB A:ASP25 4.4 8.9 1.0
ND2 A:ASN319 4.4 9.1 1.0
CB A:ASP29 4.4 7.5 1.0
O A:ASP25 4.5 9.9 1.0
O A:HOH640 4.5 19.5 1.0
O A:HOH574 4.5 15.7 1.0
OD1 A:ASP27 4.5 6.2 1.0
OD2 A:ASP303 4.8 15.3 1.0

Calcium binding site 4 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 4 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:30.0
occ:1.00
 ND2 A:ASN77 2.2 6.3 1.0
OE1 A:GLU69 2.3 4.8 1.0
O A:ILE70 2.4 8.3 1.0
OD1 A:ASP84 2.4 7.2 1.0
O A:ILE75 2.4 7.7 1.0
OD1 A:ASP73 2.4 8.4 1.0
CG A:ASP73 3.4 14.9 1.0
CG A:ASN77 3.4 15.0 1.0
CD A:GLU69 3.4 9.8 1.0
C A:ILE70 3.5 13.1 1.0
C A:ILE75 3.6 7.5 1.0
CG A:ASP84 3.6 12.8 1.0
N A:ILE70 3.7 8.8 1.0
OD2 A:ASP73 3.9 10.5 1.0
OE2 A:GLU69 4.0 6.7 1.0
N A:ILE75 4.0 9.5 1.0
CA A:ASP84 4.0 6.7 1.0
OD1 A:ASN77 4.0 10.0 1.0
CA A:ILE70 4.0 11.2 1.0
N A:ASP84 4.1 6.1 1.0
CB A:ILE70 4.2 12.0 1.0
CA A:ILE75 4.2 7.7 1.0
N A:ASN77 4.3 5.2 1.0
N A:ASP73 4.4 13.5 1.0
CB A:ASP84 4.4 9.3 1.0
CB A:ASN77 4.5 9.8 1.0
OD2 A:ASP84 4.5 11.2 1.0
CB A:ILE75 4.5 6.9 1.0
N A:ALA71 4.6 10.4 1.0
C A:GLU69 4.6 11.1 1.0
CB A:ASP73 4.6 11.8 1.0
N A:GLY74 4.6 9.9 1.0
CG A:GLU69 4.6 9.3 1.0
CB A:GLU69 4.6 9.5 1.0
N A:ASP76 4.7 8.3 1.0
CA A:GLU69 4.7 8.4 1.0
N A:GLY72 4.8 13.4 1.0
CA A:ASP73 4.8 13.4 1.0
CA A:ALA71 4.8 13.8 1.0
C A:ALA71 4.9 15.4 1.0
C A:ASP73 4.9 16.8 1.0
CA A:ASP76 4.9 6.8 1.0
CA A:ASN77 5.0 8.3 1.0

Calcium binding site 5 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 5 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:30.0
occ:1.00
 O B:HOH565 2.4 14.8 1.0
OD2 B:ASP25 2.4 5.9 1.0
O B:HOH555 2.4 9.4 1.0
O B:HOH626 2.5 12.1 1.0
OD2 B:ASP29 2.5 6.4 1.0
OD1 B:ASP25 2.6 5.8 1.0
O B:HOH518 2.6 6.0 1.0
OD1 B:ASP29 2.8 5.1 1.0
CG B:ASP25 2.8 9.4 1.0
CG B:ASP29 3.0 5.8 1.0
CA B:CA402 3.9 30.0 1.0
O B:HOH761 4.3 23.4 1.0
O B:HOH547 4.3 6.1 1.0
ND2 B:ASN319 4.4 9.9 1.0
CB B:ASP25 4.4 7.3 1.0
O B:ASP25 4.4 7.9 1.0
O B:HOH549 4.4 10.0 1.0
CB B:ASP29 4.5 5.5 1.0
OD1 B:ASP27 4.6 4.3 1.0
OD2 B:ASP303 4.7 12.2 1.0
O B:HOH880 5.0 37.8 1.0

Calcium binding site 6 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 6 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:30.0
occ:1.00
 OD1 B:ASP25 2.3 5.8 1.0
O B:HOH547 2.3 6.1 1.0
O B:HOH532 2.4 6.7 1.0
OD1 B:ASP29 2.4 5.1 1.0
O B:HOH506 2.5 6.2 1.0
OD2 B:ASP27 2.6 5.9 1.0
OD1 B:ASP27 2.7 4.3 1.0
CG B:ASP27 3.0 5.8 1.0
CG B:ASP25 3.5 9.4 1.0
CG B:ASP29 3.7 5.8 1.0
O B:HOH555 3.8 9.4 1.0
CA B:CA401 3.9 30.0 1.0
CA B:ASP25 4.0 7.9 1.0
O B:HOH518 4.1 6.0 1.0
CB B:ASP25 4.2 7.3 1.0
O B:HOH693 4.3 17.6 1.0
ND2 B:ASN15 4.3 6.9 1.0
CA B:ASP29 4.3 6.0 1.0
OE2 B:GLU32 4.3 11.7 1.0
OE1 B:GLU32 4.3 9.2 1.0
OD2 B:ASP25 4.4 5.9 1.0
OD2 B:ASP29 4.5 6.4 1.0
CB B:ASP27 4.6 5.2 1.0
CB B:ASP29 4.6 5.5 1.0
N B:ASP29 4.6 6.8 1.0
O B:ASP25 4.6 7.9 1.0
C B:ASP25 4.6 8.1 1.0
CD B:GLU32 4.6 13.2 1.0
O B:ASN16 4.8 9.1 1.0
N B:ASP25 4.9 8.1 1.0
N B:ASN16 5.0 7.3 1.0
O B:HOH676 5.0 21.9 1.0

Calcium binding site 7 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 7 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.0
occ:1.00
 OD1 B:ASP78 2.3 7.1 1.0
OE2 B:GLU69 2.3 3.8 1.0
OD1 B:ASP85 2.3 4.2 1.0
O B:TYR82 2.4 5.8 1.0
OD1 B:ASN80 2.4 5.8 1.0
OD1 B:ASP76 2.5 5.1 1.0
CD B:GLU69 3.3 9.0 1.0
CG B:ASP78 3.4 9.5 1.0
CG B:ASN80 3.4 9.8 1.0
CG B:ASP85 3.4 7.6 1.0
CG B:ASP76 3.5 9.5 1.0
C B:TYR82 3.6 9.3 1.0
CG B:GLU69 3.7 6.9 1.0
OD2 B:ASP78 3.7 10.8 1.0
OD2 B:ASP85 4.0 7.4 1.0
ND2 B:ASN80 4.0 6.2 1.0
CA B:ASP76 4.1 6.0 1.0
N B:TYR82 4.2 5.6 1.0
CB B:ASP76 4.3 8.5 1.0
N B:ASN80 4.3 6.3 1.0
CA B:TYR82 4.4 7.6 1.0
C B:ASP76 4.4 7.1 1.0
OD2 B:ASP76 4.4 7.8 1.0
OE1 B:GLU69 4.4 2.3 1.0
N B:ASP78 4.5 7.5 1.0
N B:ASP85 4.5 5.8 1.0
ND2 B:ASN66 4.5 6.5 1.0
N B:ASN77 4.6 4.8 1.0
CB B:ASN80 4.6 8.1 1.0
N B:ASP84 4.6 4.6 1.0
CB B:ASP85 4.6 5.8 1.0
N B:ILE83 4.6 6.5 1.0
CB B:TYR82 4.6 6.0 1.0
CB B:ASP78 4.7 5.5 1.0
N B:GLY79 4.7 7.9 1.0
CA B:ILE83 4.7 6.5 1.0
CA B:ASN80 4.8 6.1 1.0
CA B:ASP78 4.9 6.9 1.0
O B:ASP76 4.9 9.0 1.0
C B:ILE83 4.9 6.9 1.0
N B:GLY81 5.0 8.3 1.0

Calcium binding site 8 out of 8 in 3vv3

Go back to Calcium Binding Sites List in 3vv3
Calcium binding site 8 out of 8 in the Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Deseasin Mcp-01 From Pseudoalteromonas Sp. SM9913 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:30.0
occ:1.00
 OE1 B:GLU69 2.3 2.3 1.0
OD1 B:ASP84 2.3 6.2 1.0
O B:ILE70 2.3 6.4 1.0
OD1 B:ASN77 2.4 4.8 1.0
O B:ILE75 2.4 6.5 1.0
OD1 B:ASP73 2.5 6.2 1.0
CD B:GLU69 3.4 9.0 1.0
C B:ILE70 3.4 12.0 1.0
CG B:ASP73 3.5 13.3 1.0
CG B:ASN77 3.5 11.2 1.0
CG B:ASP84 3.5 11.4 1.0
C B:ILE75 3.6 7.1 1.0
N B:ILE70 3.8 8.8 1.0
CA B:ASP84 3.9 7.2 1.0
OE2 B:GLU69 3.9 3.8 1.0
N B:ILE75 4.0 7.0 1.0
OD2 B:ASP73 4.0 10.2 1.0
N B:ASP84 4.0 4.6 1.0
CA B:ILE70 4.1 8.3 1.0
ND2 B:ASN77 4.2 8.2 1.0
CA B:ILE75 4.2 7.0 1.0
CB B:ILE70 4.3 8.8 1.0
CB B:ASP84 4.3 6.3 1.0
N B:ASN77 4.3 4.8 1.0
N B:ASP73 4.4 7.9 1.0
OD2 B:ASP84 4.4 8.0 1.0
CB B:ILE75 4.5 6.0 1.0
N B:ALA71 4.5 9.8 1.0
CB B:GLU69 4.5 6.5 1.0
C B:GLU69 4.6 9.2 1.0
CG B:GLU69 4.6 6.9 1.0
CB B:ASN77 4.6 8.3 1.0
N B:GLY74 4.6 10.0 1.0
CB B:ASP73 4.6 12.3 1.0
N B:ASP76 4.6 7.2 1.0
CA B:GLU69 4.6 4.7 1.0
CA B:ALA71 4.8 9.5 1.0
N B:GLY72 4.8 10.4 1.0
CA B:ASP73 4.8 11.4 1.0
C B:ALA71 4.8 13.3 1.0
C B:ASP73 4.9 12.2 1.0
CA B:ASP76 4.9 6.0 1.0

Reference:

L.Y.Ran, H.N.Su, G.Y.Zhao, X.Gao, M.Y.Zhou, P.Wang, H.L.Zhao, B.B.Xie, X.Y.Zhang, X.L.Chen, B.C.Zhou, Y.Z.Zhang. Structural and Mechanistic Insights Into Collagen Degradation By A Bacterial Collagenolytic Serine Protease in the Subtilisin Family. Mol. Microbiol. V. 90 997 2013.
ISSN: ESSN 1365-2958
PubMed: 24112706
DOI: 10.1111/MMI.12412
Page generated: Sat Jul 13 20:52:48 2024

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