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Calcium in PDB 2c11: Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase

Enzymatic activity of Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase

All present enzymatic activity of Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase, PDB code: 2c11 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 / 2.90
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 127.402, 127.402, 219.361, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.6

Other elements in 2c11:

The structure of Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase also contains other interesting chemical elements:

Copper (Cu) 30 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase (pdb code 2c11). 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 the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase, PDB code: 2c11:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2c11

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Calcium binding site 1 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1736

b:52.1
occ:1.00
 O A:LEU530 2.0 57.6 1.0
OD1 A:ASP673 2.2 59.8 1.0
O A:LEU674 2.3 56.5 1.0
OD1 A:ASP531 2.5 55.9 1.0
OD1 A:ASP529 2.6 58.1 1.0
N A:LEU674 3.2 57.8 1.0
C A:LEU530 3.3 56.7 1.0
C A:LEU674 3.3 57.0 1.0
CG A:ASP673 3.4 59.8 1.0
CG A:ASP531 3.5 56.9 1.0
CG A:ASP529 3.7 57.4 1.0
NZ A:LYS106 3.7 66.4 1.0
CA A:LEU674 3.8 57.5 1.0
C A:ASP673 3.9 58.0 1.0
OD1 A:ASN537 3.9 55.6 1.0
CA A:ASP531 4.0 57.5 1.0
N A:ASP531 4.1 57.5 1.0
N A:LEU530 4.1 56.8 1.0
CA A:ASP673 4.1 59.0 1.0
OD2 A:ASP673 4.2 60.3 1.0
OD2 A:ASP531 4.2 57.9 1.0
C A:ASP529 4.2 56.9 1.0
OD2 A:ASP529 4.3 58.2 1.0
CA A:LEU530 4.3 56.2 1.0
CB A:ASP531 4.4 57.4 1.0
CB A:ASP673 4.4 59.4 1.0
O A:LEU535 4.5 59.5 1.0
O A:ASP529 4.5 57.0 1.0
N A:VAL675 4.5 56.0 1.0
O A:ASP673 4.7 57.8 1.0
CA A:ASP529 4.7 55.5 1.0
CB A:LEU674 4.8 57.6 1.0
CB A:ARG637 4.8 65.7 1.0
CB A:ASP529 4.8 56.5 1.0
CA A:VAL675 5.0 55.5 1.0

Calcium binding site 2 out of 8 in 2c11

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Calcium binding site 2 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1738

b:49.6
occ:1.00
 OE1 A:GLU572 2.2 65.7 1.0
O A:HOH2014 2.3 35.6 1.0
OD1 A:ASN665 2.4 65.9 1.0
OE2 A:GLU572 2.7 66.2 1.0
NZ A:LYS638 2.8 67.1 1.0
CD A:GLU572 2.8 66.0 1.0
O A:PHE663 3.0 64.9 1.0
OE2 A:GLU667 3.2 67.6 1.0
CD A:GLU667 3.3 67.0 1.0
CG A:ASN665 3.4 67.5 1.0
OE1 A:GLU667 3.6 67.0 1.0
ND2 A:ASN665 3.8 67.5 1.0
CE A:LYS638 3.9 65.4 1.0
OE1 A:GLU641 3.9 68.6 1.0
C A:PHE663 4.0 65.5 1.0
CG A:GLU667 4.1 67.3 1.0
OE2 A:GLU641 4.2 66.7 1.0
CG A:GLU572 4.3 66.4 1.0
CB A:THR635 4.4 59.4 1.0
CB A:GLU667 4.4 67.3 1.0
CD A:GLU641 4.5 67.9 1.0
N A:ASN665 4.5 66.2 1.0
N A:GLN636 4.6 60.1 1.0
CG2 A:THR635 4.7 58.5 1.0
CB A:GLN636 4.7 61.9 1.0
CD A:LYS638 4.7 65.1 1.0
CA A:PHE663 4.7 65.3 1.0
CB A:ASN665 4.8 66.5 1.0
N A:ILE664 4.9 66.7 1.0
O A:ASN665 4.9 69.2 1.0
CA A:ILE664 5.0 65.7 1.0

Calcium binding site 3 out of 8 in 2c11

Go back to Calcium Binding Sites List in 2c11
Calcium binding site 3 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1741

b:46.8
occ:1.00
 O B:LEU530 2.2 49.4 1.0
O B:LEU674 2.3 52.0 1.0
OD1 B:ASP673 2.3 55.9 1.0
OD1 B:ASP531 2.4 48.2 1.0
OD1 B:ASP529 2.8 49.8 1.0
C B:LEU530 3.3 48.9 1.0
N B:LEU674 3.4 52.7 1.0
CG B:ASP673 3.4 54.5 1.0
C B:LEU674 3.4 51.9 1.0
NZ B:LYS106 3.6 59.2 1.0
CG B:ASP531 3.7 48.2 1.0
CG B:ASP529 3.9 48.4 1.0
C B:ASP673 3.9 54.4 1.0
CA B:LEU674 4.0 51.7 1.0
OD2 B:ASP673 4.1 55.0 1.0
C B:ASP529 4.1 48.9 1.0
OD1 B:ASN537 4.1 48.2 1.0
N B:ASP531 4.2 49.0 1.0
N B:LEU530 4.2 49.0 1.0
CA B:ASP673 4.2 55.5 1.0
CA B:ASP531 4.2 50.3 1.0
O B:ASP529 4.2 48.2 1.0
O B:LEU535 4.3 50.2 1.0
CA B:LEU530 4.3 48.0 1.0
CB B:ASP673 4.4 55.0 1.0
OD2 B:ASP531 4.5 48.9 1.0
N B:VAL675 4.5 51.5 1.0
OD2 B:ASP529 4.5 49.4 1.0
CB B:ASP531 4.6 48.8 1.0
CD2 B:LEU535 4.6 48.4 1.0
CA B:ASP529 4.7 48.5 1.0
O B:ASP673 4.7 54.5 1.0
CB B:LEU674 4.9 51.5 1.0
CB B:ASP529 4.9 47.2 1.0
CA B:VAL675 4.9 51.4 1.0
CG B:ARG637 5.0 57.5 1.0
CB B:ARG637 5.0 58.2 1.0

Calcium binding site 4 out of 8 in 2c11

Go back to Calcium Binding Sites List in 2c11
Calcium binding site 4 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1743

b:47.3
occ:1.00
 OE1 B:GLU667 2.0 67.5 1.0
OE1 B:GLU572 2.4 59.4 1.0
OD1 B:ASN665 2.5 64.6 1.0
O B:PHE663 2.5 64.3 1.0
OE2 B:GLU572 2.7 59.9 1.0
CD B:GLU667 2.9 67.4 1.0
CD B:GLU572 2.9 60.5 1.0
CG B:ASN665 3.5 65.0 1.0
C B:PHE663 3.5 63.8 1.0
CE B:LYS638 3.6 59.8 1.0
OE2 B:GLU667 3.6 67.6 1.0
CG B:GLU667 3.8 67.2 1.0
ND2 B:ASN665 3.9 65.6 1.0
N B:ASN665 4.3 66.4 1.0
CA B:PHE663 4.3 63.2 1.0
CB B:GLU667 4.4 67.6 1.0
OE1 B:GLU641 4.4 60.1 1.0
CG B:GLU572 4.4 59.7 1.0
N B:ILE664 4.4 64.6 1.0
CB B:THR635 4.5 54.7 1.0
NZ B:LYS638 4.5 60.7 1.0
OE2 B:GLU641 4.5 59.1 1.0
CA B:ILE664 4.6 64.6 1.0
O B:ASN665 4.6 69.0 1.0
N B:GLN636 4.7 55.4 1.0
CD B:LYS638 4.8 60.4 1.0
CB B:ASN665 4.8 66.4 1.0
C B:ILE664 4.9 64.9 1.0
CD B:GLU641 4.9 59.4 1.0
CB B:GLN636 4.9 56.2 1.0
CG B:GLN636 4.9 59.1 1.0
O B:GLN636 5.0 56.0 1.0
CG2 B:THR635 5.0 54.1 1.0

Calcium binding site 5 out of 8 in 2c11

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Calcium binding site 5 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1737

b:50.3
occ:1.00
 OD1 C:ASP673 2.1 60.0 1.0
O C:LEU530 2.1 57.4 1.0
O C:LEU674 2.2 56.1 1.0
OD1 C:ASP529 2.4 57.9 1.0
OD1 C:ASP531 2.8 56.2 1.0
N C:LEU674 3.3 59.1 1.0
C C:LEU530 3.3 57.1 1.0
CG C:ASP673 3.3 59.9 1.0
C C:LEU674 3.3 56.5 1.0
CG C:ASP529 3.5 56.9 1.0
NZ C:LYS106 3.7 66.5 1.0
CG C:ASP531 3.8 57.0 1.0
CA C:LEU674 3.8 57.2 1.0
C C:ASP673 3.9 59.2 1.0
N C:LEU530 3.9 56.8 1.0
OD2 C:ASP673 4.0 60.0 1.0
C C:ASP529 4.1 56.5 1.0
OD1 C:ASN537 4.1 56.2 1.0
CA C:ASP673 4.1 59.4 1.0
N C:ASP531 4.2 58.6 1.0
OD2 C:ASP529 4.2 57.3 1.0
CA C:LEU530 4.2 56.7 1.0
CA C:ASP531 4.2 58.6 1.0
CB C:ASP673 4.3 59.8 1.0
O C:ASP529 4.4 56.5 1.0
OD2 C:ASP531 4.4 59.6 1.0
N C:VAL675 4.5 56.6 1.0
CA C:ASP529 4.5 56.2 1.0
O C:LEU535 4.5 60.4 1.0
CB C:ASP529 4.6 57.0 1.0
CB C:ASP531 4.6 57.0 1.0
CB C:ARG637 4.7 66.0 1.0
O C:ASP673 4.8 59.0 1.0
CB C:LEU674 4.8 58.2 1.0
CA C:VAL675 4.8 55.6 1.0

Calcium binding site 6 out of 8 in 2c11

Go back to Calcium Binding Sites List in 2c11
Calcium binding site 6 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1739

b:50.2
occ:1.00
 OD1 C:ASN665 2.1 66.6 1.0
NZ C:LYS638 2.5 65.7 1.0
OE1 C:GLU572 2.6 66.0 1.0
OE2 C:GLU572 2.7 67.5 1.0
O C:PHE663 2.9 64.7 1.0
CD C:GLU572 3.0 66.6 1.0
CG C:ASN665 3.0 68.3 1.0
OE1 C:GLU667 3.3 68.7 1.0
CD C:GLU667 3.3 68.0 1.0
ND2 C:ASN665 3.3 68.5 1.0
OE2 C:GLU667 3.4 68.3 1.0
CE C:LYS638 3.6 64.8 1.0
OE2 C:GLU641 3.8 67.3 1.0
C C:PHE663 3.9 65.5 1.0
OE1 C:GLU641 3.9 69.1 1.0
CG C:GLU667 4.1 67.8 1.0
CD C:GLU641 4.3 68.5 1.0
N C:ASN665 4.4 67.8 1.0
CB C:ASN665 4.5 67.4 1.0
CG C:GLU572 4.5 66.1 1.0
CB C:GLU667 4.5 67.3 1.0
CB C:THR635 4.5 59.8 1.0
CD C:LYS638 4.6 64.7 1.0
CA C:PHE663 4.7 65.5 1.0
N C:ILE664 4.8 66.6 1.0
N C:GLN636 4.8 61.0 1.0
O C:ASN665 4.9 70.3 1.0
CB C:GLN636 4.9 61.3 1.0
CG2 C:THR635 4.9 58.8 1.0
CA C:ILE664 5.0 66.1 1.0

Calcium binding site 7 out of 8 in 2c11

Go back to Calcium Binding Sites List in 2c11
Calcium binding site 7 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1741

b:47.7
occ:1.00
 O D:LEU530 2.3 49.1 1.0
OD1 D:ASP673 2.3 56.5 1.0
OD1 D:ASP531 2.4 49.8 1.0
O D:LEU674 2.4 51.3 1.0
OD1 D:ASP529 2.5 49.1 1.0
C D:LEU530 3.4 48.6 1.0
C D:LEU674 3.5 52.1 1.0
N D:LEU674 3.5 53.7 1.0
NZ D:LYS106 3.5 58.7 1.0
CG D:ASP673 3.5 54.7 1.0
CG D:ASP531 3.6 50.0 1.0
CG D:ASP529 3.7 49.1 1.0
C D:ASP673 4.0 55.1 1.0
C D:ASP529 4.0 49.2 1.0
CA D:LEU674 4.0 52.3 1.0
O D:ASP529 4.0 49.5 1.0
OD2 D:ASP673 4.2 54.6 1.0
N D:ASP531 4.2 48.8 1.0
N D:LEU530 4.2 49.0 1.0
CA D:ASP531 4.2 49.9 1.0
OD1 D:ASN537 4.2 48.5 1.0
CA D:ASP673 4.2 55.9 1.0
O D:LEU535 4.4 50.2 1.0
OD2 D:ASP529 4.4 49.8 1.0
CA D:LEU530 4.4 48.0 1.0
OD2 D:ASP531 4.4 50.2 1.0
CB D:ASP673 4.4 54.9 1.0
CB D:ASP531 4.5 50.3 1.0
CA D:ASP529 4.5 48.1 1.0
N D:VAL675 4.6 52.5 1.0
CD2 D:LEU535 4.6 48.3 1.0
CB D:ASP529 4.7 48.7 1.0
O D:ASP673 4.7 54.9 1.0
CB D:LEU674 4.9 52.6 1.0
CE D:LYS106 4.9 59.3 1.0
CB D:ARG637 4.9 57.5 1.0
CA D:VAL675 5.0 51.5 1.0

Calcium binding site 8 out of 8 in 2c11

Go back to Calcium Binding Sites List in 2c11
Calcium binding site 8 out of 8 in the Crystal Structure of the 2-Hydrazinopyridine 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 Crystal Structure of the 2-Hydrazinopyridine of Semicarbazide- Sensitive Amine Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1743

b:46.7
occ:1.00
 O D:PHE663 2.2 64.8 1.0
OE1 D:GLU667 2.2 68.3 1.0
OD1 D:ASN665 2.3 65.8 1.0
OE2 D:GLU572 2.5 59.4 1.0
OE1 D:GLU572 2.5 59.2 1.0
CD D:GLU572 2.8 60.0 1.0
C D:PHE663 3.2 63.8 1.0
CD D:GLU667 3.3 67.3 1.0
CG D:ASN665 3.3 66.0 1.0
ND2 D:ASN665 3.8 65.4 1.0
N D:ASN665 4.0 65.9 1.0
CG D:GLU667 4.1 66.8 1.0
CA D:PHE663 4.1 63.3 1.0
OE2 D:GLU667 4.1 66.7 1.0
N D:ILE664 4.1 64.3 1.0
CE D:LYS638 4.3 60.5 1.0
CA D:ILE664 4.3 64.7 1.0
CG D:GLU572 4.3 59.4 1.0
O D:ASN665 4.5 68.8 1.0
OE1 D:GLU641 4.5 59.0 1.0
CB D:THR635 4.5 54.0 1.0
OE2 D:GLU641 4.6 58.3 1.0
CB D:GLU667 4.6 67.1 1.0
C D:ILE664 4.6 65.1 1.0
CB D:ASN665 4.6 66.9 1.0
CA D:ASN665 4.8 67.0 1.0
CB D:PHE663 4.8 62.9 1.0
N D:GLN636 4.8 54.6 1.0
CG2 D:THR635 4.8 53.2 1.0
CD D:GLU641 5.0 59.0 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 09:16:52 2024

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