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Calcium in PDB 2c10: The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase

Enzymatic activity of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase

All present enzymatic activity of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase:
1.4.3.6;

Protein crystallography data

The structure of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase, PDB code: 2c10 was solved by E.Jakobsson, G.J.Kleywegt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 130.236, 130.236, 221.529, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.2

Other elements in 2c10:

The structure of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase also contains other interesting chemical elements:

Copper (Cu) 4 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase (pdb code 2c10). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase, PDB code: 2c10:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2c10

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Calcium binding site 1 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1771

b:29.2
occ:1.00
 O A:LEU530 2.3 32.2 1.0
OD1 A:ASP529 2.3 35.2 1.0
OD1 A:ASP531 2.3 34.3 1.0
O A:LEU674 2.4 29.4 1.0
O A:HOH2105 2.5 24.4 1.0
OD1 A:ASP673 2.5 30.5 1.0
C A:LEU530 3.3 32.7 1.0
C A:LEU674 3.5 29.4 1.0
N A:LEU674 3.5 29.8 1.0
CG A:ASP531 3.6 34.4 1.0
CG A:ASP529 3.6 34.0 1.0
CG A:ASP673 3.7 30.4 1.0
NZ A:LYS106 3.9 28.9 1.0
CA A:ASP531 3.9 33.9 1.0
N A:ASP531 3.9 33.3 1.0
CA A:LEU674 4.1 29.1 1.0
N A:LEU530 4.2 32.8 1.0
C A:ASP529 4.2 32.4 1.0
C A:ASP673 4.2 30.5 1.0
OD2 A:ASP529 4.3 33.7 1.0
CB A:ASP531 4.3 34.0 1.0
CA A:LEU530 4.4 32.6 1.0
OD2 A:ASP673 4.4 30.3 1.0
CA A:ASP673 4.5 30.8 1.0
CA A:ASP529 4.5 32.1 1.0
OD2 A:ASP531 4.5 35.1 1.0
O A:LEU535 4.5 34.7 1.0
OD1 A:ASN537 4.6 31.3 1.0
O A:ASP529 4.6 32.5 1.0
N A:VAL675 4.6 29.6 1.0
CB A:ASP529 4.7 32.4 1.0
CB A:ASP673 4.7 30.6 1.0
CB A:LEU674 4.8 28.3 1.0

Calcium binding site 2 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 2 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1773

b:40.8
occ:1.00
 O A:PHE663 2.3 36.7 1.0
OD1 A:ASN665 2.4 39.4 1.0
OE2 A:GLU572 2.5 37.4 1.0
O A:HOH2125 2.5 24.5 1.0
OE1 A:GLU572 2.6 37.9 1.0
OE1 A:GLU667 2.6 37.7 1.0
CD A:GLU572 2.9 38.1 1.0
CD A:GLU667 3.5 38.9 1.0
C A:PHE663 3.5 36.4 1.0
CG A:ASN665 3.5 39.6 1.0
CG A:GLU667 3.9 38.6 1.0
ND2 A:ASN665 4.1 40.7 1.0
NZ A:LYS638 4.1 34.9 1.0
N A:ASN665 4.1 38.3 1.0
CA A:PHE663 4.3 36.3 1.0
OE2 A:GLU667 4.4 38.5 1.0
CB A:GLU667 4.4 38.4 1.0
N A:ILE664 4.4 36.5 1.0
CG A:GLU572 4.4 38.2 1.0
CA A:ILE664 4.5 36.4 1.0
OE1 A:GLU641 4.6 38.1 1.0
CE A:LYS638 4.6 35.1 1.0
OE2 A:GLU641 4.6 38.2 1.0
CB A:THR635 4.6 31.6 1.0
C A:ILE664 4.8 37.3 1.0
CB A:ASN665 4.8 39.2 1.0
N A:GLN636 4.8 32.4 1.0
CB A:PHE663 4.9 36.1 1.0
CG2 A:THR635 4.9 31.9 1.0
CA A:ASN665 5.0 39.1 1.0

Calcium binding site 3 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 3 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1775

b:27.3
occ:1.00
 OD1 B:ASP673 2.2 28.4 1.0
O B:LEU674 2.3 28.8 1.0
O B:HOH2095 2.3 24.6 1.0
O B:LEU530 2.3 29.5 1.0
OD1 B:ASP529 2.4 32.4 1.0
OD1 B:ASP531 2.4 30.9 1.0
N B:LEU674 3.3 28.2 1.0
C B:LEU674 3.4 28.7 1.0
C B:LEU530 3.4 29.4 1.0
CG B:ASP673 3.5 28.4 1.0
CG B:ASP529 3.6 30.6 1.0
CG B:ASP531 3.6 30.6 1.0
NZ B:LYS106 3.8 24.3 1.0
CA B:LEU674 3.9 28.1 1.0
C B:ASP673 4.0 28.1 1.0
N B:ASP531 4.1 29.4 1.0
CA B:ASP531 4.1 29.9 1.0
C B:ASP529 4.2 29.7 1.0
CA B:ASP673 4.2 28.1 1.0
N B:LEU530 4.2 29.7 1.0
OD2 B:ASP673 4.3 27.8 1.0
OD2 B:ASP529 4.3 31.0 1.0
O B:LEU535 4.3 31.1 1.0
CA B:LEU530 4.4 29.3 1.0
O B:ASP529 4.5 29.8 1.0
CB B:ASP531 4.5 29.7 1.0
CB B:ASP673 4.5 27.9 1.0
N B:VAL675 4.5 28.9 1.0
OD2 B:ASP531 4.5 31.7 1.0
CA B:ASP529 4.5 29.7 1.0
OD1 B:ASN537 4.6 26.7 1.0
CB B:LEU674 4.7 27.8 1.0
CB B:ASP529 4.7 29.7 1.0
O B:ASP673 4.9 28.4 1.0
CA B:VAL675 4.9 29.2 1.0

Calcium binding site 4 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 4 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1777

b:31.9
occ:1.00
 O B:PHE663 2.3 34.1 1.0
O B:HOH2120 2.3 32.7 1.0
OD1 B:ASN665 2.3 36.9 1.0
OE1 B:GLU667 2.3 39.4 1.0
O B:HOH2117 2.4 16.0 1.0
OE2 B:GLU572 2.6 36.8 1.0
OE1 B:GLU572 2.7 35.5 1.0
CD B:GLU572 3.0 35.1 1.0
CG B:ASN665 3.4 39.1 1.0
C B:PHE663 3.4 34.0 1.0
CD B:GLU667 3.5 38.9 1.0
ND2 B:ASN665 3.9 40.5 1.0
N B:ASN665 4.1 36.9 1.0
CB B:GLU667 4.2 36.7 1.0
NZ B:LYS638 4.2 35.1 1.0
OE2 B:GLU667 4.3 38.8 1.0
CA B:PHE663 4.3 33.9 1.0
CG B:GLU667 4.3 37.7 1.0
N B:ILE664 4.4 34.2 1.0
OE2 B:GLU641 4.5 36.0 1.0
CG B:GLU572 4.5 35.1 1.0
CB B:THR635 4.6 32.6 1.0
CA B:ILE664 4.6 34.7 1.0
CE B:LYS638 4.6 37.6 1.0
OE1 B:GLU641 4.6 34.5 1.0
CB B:ASN665 4.7 38.3 1.0
C B:ILE664 4.8 35.8 1.0
CG2 B:THR635 4.8 31.6 1.0
N B:GLN636 4.8 33.5 1.0
CA B:ASN665 4.8 38.3 1.0
CB B:GLN636 5.0 33.9 1.0
O B:GLN636 5.0 34.4 1.0
O B:ASP662 5.0 34.4 1.0

Calcium binding site 5 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 5 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1771

b:28.3
occ:1.00
 OD1 C:ASP529 2.2 32.7 1.0
O C:LEU530 2.3 27.8 1.0
OD1 C:ASP531 2.3 31.6 1.0
O C:LEU674 2.3 28.6 1.0
O C:HOH2121 2.4 23.9 1.0
OD1 C:ASP673 2.4 31.4 1.0
C C:LEU530 3.2 28.4 1.0
C C:LEU674 3.4 28.9 1.0
CG C:ASP529 3.5 29.6 1.0
CG C:ASP531 3.5 31.2 1.0
N C:LEU674 3.6 29.6 1.0
CG C:ASP673 3.7 30.5 1.0
NZ C:LYS106 3.9 31.7 1.0
N C:ASP531 3.9 29.5 1.0
CA C:ASP531 3.9 30.6 1.0
C C:ASP529 4.0 28.0 1.0
CA C:LEU674 4.1 28.9 1.0
N C:LEU530 4.1 28.1 1.0
OD2 C:ASP529 4.2 30.9 1.0
O C:ASP529 4.2 28.2 1.0
C C:ASP673 4.3 30.2 1.0
CB C:ASP531 4.3 30.5 1.0
CA C:ASP529 4.3 28.2 1.0
CA C:LEU530 4.3 28.2 1.0
OD2 C:ASP673 4.3 31.2 1.0
OD1 C:ASN537 4.4 31.7 1.0
OD2 C:ASP531 4.4 31.2 1.0
CB C:ASP529 4.5 27.9 1.0
N C:VAL675 4.5 28.6 1.0
CA C:ASP673 4.6 30.8 1.0
O C:LEU535 4.6 34.5 1.0
CB C:ASP673 4.7 30.4 1.0
CB C:LEU674 4.8 28.1 1.0
CA C:VAL675 4.9 28.8 1.0

Calcium binding site 6 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 6 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1773

b:42.4
occ:1.00
 OD1 C:ASN665 2.3 41.2 1.0
O C:PHE663 2.4 38.0 1.0
OE1 C:GLU572 2.6 36.2 1.0
OE1 C:GLU667 2.6 38.9 1.0
OE2 C:GLU572 2.6 35.2 1.0
CD C:GLU572 2.9 36.2 1.0
CD C:GLU667 3.4 39.7 1.0
CG C:ASN665 3.5 41.6 1.0
C C:PHE663 3.5 37.9 1.0
CG C:GLU667 4.0 39.7 1.0
N C:ASN665 4.1 40.5 1.0
ND2 C:ASN665 4.1 42.1 1.0
NZ C:LYS638 4.2 36.9 1.0
CA C:PHE663 4.3 37.5 1.0
OE2 C:GLU667 4.3 39.7 1.0
CB C:GLU667 4.4 39.9 1.0
CG C:GLU572 4.5 36.3 1.0
N C:ILE664 4.5 38.6 1.0
CB C:THR635 4.5 28.9 1.0
OE1 C:GLU641 4.5 36.1 1.0
CE C:LYS638 4.6 35.4 1.0
CA C:ILE664 4.6 39.0 1.0
OE2 C:GLU641 4.7 38.7 1.0
CG2 C:THR635 4.7 28.3 1.0
CB C:ASN665 4.7 41.0 1.0
N C:GLN636 4.8 30.7 1.0
CA C:ASN665 4.9 41.0 1.0
C C:ILE664 4.9 39.9 1.0
O C:ASN665 5.0 42.0 1.0
CB C:PHE663 5.0 36.8 1.0

Calcium binding site 7 out of 8 in 2c10

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Calcium binding site 7 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1776

b:25.0
occ:1.00
 OD1 D:ASP673 2.2 28.4 1.0
OD1 D:ASP531 2.2 31.5 1.0
O D:LEU530 2.3 28.2 1.0
OD1 D:ASP529 2.3 29.4 1.0
O D:LEU674 2.4 29.7 1.0
O D:HOH2092 2.4 14.3 1.0
N D:LEU674 3.3 28.9 1.0
C D:LEU530 3.4 28.0 1.0
CG D:ASP673 3.4 29.4 1.0
C D:LEU674 3.4 29.4 1.0
CG D:ASP531 3.5 30.5 1.0
CG D:ASP529 3.5 28.3 1.0
NZ D:LYS106 3.9 29.8 1.0
CA D:LEU674 4.0 29.1 1.0
CA D:ASP531 4.0 28.9 1.0
N D:ASP531 4.0 28.3 1.0
C D:ASP673 4.0 29.1 1.0
OD2 D:ASP673 4.1 29.1 1.0
OD2 D:ASP529 4.2 28.6 1.0
C D:ASP529 4.2 27.7 1.0
CA D:ASP673 4.3 29.4 1.0
CB D:ASP531 4.3 28.9 1.0
OD2 D:ASP531 4.4 33.0 1.0
N D:LEU530 4.4 27.9 1.0
O D:LEU535 4.4 30.7 1.0
CB D:ASP673 4.4 29.5 1.0
O D:ASP529 4.4 27.4 1.0
CA D:LEU530 4.5 27.6 1.0
CA D:ASP529 4.6 27.6 1.0
N D:VAL675 4.6 29.4 1.0
OD1 D:ASN537 4.7 28.6 1.0
CB D:ASP529 4.7 27.8 1.0
CB D:LEU674 4.8 28.6 1.0
CD2 D:LEU535 4.9 32.4 1.0
O D:ASP673 4.9 28.3 1.0
CA D:VAL675 5.0 29.6 1.0

Calcium binding site 8 out of 8 in 2c10

Go back to Calcium Binding Sites List in 2c10
Calcium binding site 8 out of 8 in the The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of A Truncated, Soluble Version of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1778

b:29.1
occ:1.00
 O D:PHE663 2.2 34.9 1.0
O D:HOH2114 2.4 19.1 1.0
OE1 D:GLU667 2.4 37.4 1.0
O D:HOH2113 2.5 25.1 1.0
OE2 D:GLU572 2.5 36.9 1.0
OD1 D:ASN665 2.7 40.9 1.0
OE1 D:GLU572 2.8 37.0 1.0
CD D:GLU572 3.0 36.2 1.0
C D:PHE663 3.3 34.7 1.0
CG D:ASN665 3.4 40.1 1.0
CD D:GLU667 3.4 37.1 1.0
ND2 D:ASN665 3.6 41.0 1.0
N D:ASN665 3.8 37.6 1.0
CG D:GLU667 4.1 36.5 1.0
CA D:PHE663 4.2 34.8 1.0
CB D:GLU667 4.2 36.0 1.0
N D:ILE664 4.3 35.2 1.0
OE2 D:GLU667 4.4 37.3 1.0
CA D:ILE664 4.5 35.6 1.0
NZ D:LYS638 4.5 34.2 1.0
OE2 D:GLU641 4.5 35.7 1.0
CG D:GLU572 4.5 36.0 1.0
CB D:ASN665 4.6 39.2 1.0
CA D:ASN665 4.6 38.8 1.0
C D:ILE664 4.6 36.7 1.0
CB D:THR635 4.7 30.0 1.0
O D:ASP662 4.7 35.7 1.0
CE D:LYS638 4.7 34.6 1.0
OE1 D:GLU641 4.8 36.2 1.0
CG2 D:THR635 4.9 28.8 1.0
N D:GLN636 5.0 30.9 1.0
C D:ASN665 5.0 39.3 1.0

Reference:

E.Jakobsson, J.Nilsson, D.Ogg, G.J.Kleywegt. Structure of Human Semicarbazide-Sensitive Amine Oxidase/Vascular Adhesion Protein-1. Acta Crystallogr. D Biol. V. 61 1550 2005CRYSTALLOGR..
ISSN: ISSN 0907-4449
PubMed: 16239734
DOI: 10.1107/S0907444905028805
Page generated: Fri Jul 12 09:16:34 2024

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