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Sodium in PDB 2wc8: S100A12 Complex with Zinc in the Absence of Calcium

Protein crystallography data

The structure of S100A12 Complex with Zinc in the Absence of Calcium, PDB code: 2wc8 was solved by O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.991, 81.830, 85.725, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 23.6

Other elements in 2wc8:

The structure of S100A12 Complex with Zinc in the Absence of Calcium also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the S100A12 Complex with Zinc in the Absence of Calcium (pdb code 2wc8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the S100A12 Complex with Zinc in the Absence of Calcium, PDB code: 2wc8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2wc8

Go back to Sodium Binding Sites List in 2wc8
Sodium binding site 1 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na92

b:12.8
occ:1.00
O A:HOH2042 2.3 21.4 1.0
O A:LYS21 2.3 13.1 1.0
O A:THR26 2.3 13.5 1.0
O A:SER18 2.4 11.2 1.0
O A:HIS23 2.4 12.3 1.0
O A:HOH2063 2.5 11.4 1.0
C A:SER18 3.5 13.2 1.0
C A:LYS21 3.5 14.2 1.0
C A:HIS23 3.6 12.3 1.0
C A:THR26 3.6 15.3 1.0
CA A:SER18 4.0 14.1 1.0
N A:LYS21 4.0 14.1 1.0
N A:HIS23 4.1 13.7 1.0
C A:GLY22 4.2 13.1 1.0
CA A:LYS21 4.3 14.5 1.0
CA A:LEU27 4.3 17.3 1.0
N A:THR26 4.4 13.4 1.0
CA A:HIS23 4.4 13.2 1.0
N A:LEU27 4.4 15.6 1.0
N A:PHE24 4.4 12.7 1.0
N A:GLY22 4.5 13.1 1.0
OE1 A:GLN67 4.5 20.1 1.0
O A:HOH2048 4.5 6.5 1.0
CA A:PHE24 4.5 12.1 1.0
CA A:THR26 4.5 13.2 1.0
OE1 A:GLU31 4.5 16.0 1.0
CA A:GLY22 4.6 13.4 1.0
N A:VAL19 4.6 13.0 1.0
O A:GLY22 4.6 11.0 1.0
CB A:SER18 4.6 14.8 1.0
C A:PHE24 4.7 12.3 1.0
N A:ARG20 4.7 12.2 1.0
C A:VAL19 4.8 11.6 1.0
CB A:LYS21 4.8 15.8 1.0
OG1 A:THR26 4.8 13.8 1.0
O A:TYR17 4.8 15.8 1.0
OE2 A:GLU31 4.9 18.5 1.0
CB A:LEU27 4.9 19.4 1.0
CA A:VAL19 4.9 11.6 1.0
O A:PHE24 5.0 12.8 1.0
N A:ASP25 5.0 11.8 1.0

Sodium binding site 2 out of 4 in 2wc8

Go back to Sodium Binding Sites List in 2wc8
Sodium binding site 2 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na92

b:8.9
occ:1.00
O C:HIS23 2.1 14.5 1.0
O C:HOH2092 2.3 14.3 1.0
O C:THR26 2.3 13.5 1.0
O C:SER18 2.3 12.1 1.0
O C:LYS21 2.4 13.2 1.0
O C:HOH2051 2.6 13.0 1.0
C C:HIS23 3.3 15.1 1.0
C C:SER18 3.4 13.3 1.0
C C:THR26 3.5 14.8 1.0
C C:LYS21 3.5 14.7 1.0
CA C:SER18 3.8 13.5 1.0
N C:HIS23 3.9 15.8 1.0
N C:LYS21 4.2 13.5 1.0
N C:THR26 4.2 13.6 1.0
CA C:HIS23 4.2 15.2 1.0
N C:PHE24 4.2 14.4 1.0
CA C:LEU27 4.2 15.3 1.0
C C:GLY22 4.2 16.1 1.0
CA C:PHE24 4.3 14.8 1.0
N C:LEU27 4.3 15.1 1.0
O C:HOH2049 4.4 14.6 1.0
C C:PHE24 4.4 13.1 1.0
OE1 C:GLN67 4.4 18.0 1.0
CA C:LYS21 4.4 14.8 1.0
CA C:THR26 4.5 13.4 1.0
N C:GLY22 4.5 15.0 1.0
CB C:SER18 4.5 14.9 1.0
CA C:GLY22 4.5 15.8 1.0
N C:VAL19 4.6 11.7 1.0
OG1 C:THR26 4.6 14.7 1.0
O C:TYR17 4.6 13.4 1.0
N C:ARG20 4.7 10.3 1.0
O C:PHE24 4.8 12.1 1.0
O C:GLY22 4.8 17.5 1.0
O C:HOH2029 4.8 19.7 1.0
N C:ASP25 4.8 12.2 1.0
CB C:LEU27 4.8 17.8 1.0
C C:VAL19 4.9 11.3 1.0

Sodium binding site 3 out of 4 in 2wc8

Go back to Sodium Binding Sites List in 2wc8
Sodium binding site 3 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na92

b:10.3
occ:1.00
O B:LYS21 2.2 12.2 1.0
O B:HOH2108 2.2 15.9 1.0
O B:HIS23 2.3 10.7 1.0
O B:SER18 2.4 10.2 1.0
O B:HOH2055 2.4 14.0 1.0
O B:THR26 2.4 13.0 1.0
C B:LYS21 3.4 13.2 1.0
C B:SER18 3.4 11.4 1.0
C B:HIS23 3.4 12.0 1.0
C B:THR26 3.6 13.5 1.0
CA B:SER18 3.9 11.1 1.0
N B:HIS23 3.9 12.3 1.0
N B:LYS21 4.0 13.3 1.0
C B:GLY22 4.1 12.3 1.0
CA B:LYS21 4.2 13.9 1.0
N B:THR26 4.2 14.7 1.0
CA B:HIS23 4.3 11.5 1.0
N B:GLY22 4.3 11.8 1.0
N B:PHE24 4.3 12.5 1.0
O B:HOH2056 4.3 14.7 1.0
CA B:GLY22 4.4 12.3 1.0
CA B:LEU27 4.4 14.0 1.0
N B:LEU27 4.4 13.3 1.0
CA B:PHE24 4.4 13.3 1.0
CA B:THR26 4.5 13.7 1.0
OG1 B:THR26 4.5 13.4 1.0
OE1 B:GLN67 4.5 14.2 1.0
C B:PHE24 4.5 13.6 1.0
CB B:SER18 4.6 11.3 1.0
N B:VAL19 4.6 11.4 1.0
O B:GLY22 4.6 12.6 1.0
O B:TYR17 4.7 10.9 1.0
N B:ARG20 4.7 12.2 1.0
O B:HOH2041 4.8 20.7 1.0
OE2 B:GLU31 4.8 16.7 1.0
N B:ASP25 4.9 14.1 1.0
O B:PHE24 4.9 14.3 1.0
O B:HOH2032 4.9 19.2 1.0
C B:VAL19 4.9 12.6 1.0

Sodium binding site 4 out of 4 in 2wc8

Go back to Sodium Binding Sites List in 2wc8
Sodium binding site 4 out of 4 in the S100A12 Complex with Zinc in the Absence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of S100A12 Complex with Zinc in the Absence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na92

b:14.1
occ:1.00
O D:HIS23 2.2 13.2 1.0
O D:SER18 2.2 11.6 1.0
O D:THR26 2.3 13.6 1.0
O D:LYS21 2.4 15.0 1.0
O D:HOH2110 2.4 14.0 1.0
O D:HOH2057 2.5 13.5 1.0
C D:SER18 3.3 12.5 1.0
C D:HIS23 3.4 14.2 1.0
C D:THR26 3.5 13.6 1.0
C D:LYS21 3.6 15.4 1.0
N D:HIS23 3.7 15.5 1.0
CA D:SER18 3.9 12.5 1.0
CA D:HIS23 4.1 15.1 1.0
N D:LYS21 4.2 13.5 1.0
C D:GLY22 4.2 16.3 1.0
CA D:LEU27 4.2 13.7 1.0
O D:HOH2035 4.2 22.1 1.0
N D:LEU27 4.3 13.2 1.0
O D:HOH2060 4.3 16.1 1.0
N D:THR26 4.4 14.8 1.0
CB D:SER18 4.5 12.9 1.0
N D:PHE24 4.5 14.2 1.0
N D:VAL19 4.5 13.0 1.0
CA D:LYS21 4.5 16.0 1.0
N D:GLY22 4.5 16.0 1.0
CA D:GLY22 4.5 16.1 1.0
OE1 D:GLN67 4.5 13.2 1.0
CA D:THR26 4.6 13.9 1.0
CB D:HIS23 4.6 14.0 1.0
C D:PHE24 4.6 14.5 1.0
O D:PHE24 4.6 14.4 1.0
O D:TYR17 4.7 13.3 1.0
CA D:PHE24 4.7 13.9 1.0
CB D:LEU27 4.7 13.2 1.0
O D:GLY22 4.8 17.3 1.0
CA D:VAL19 4.8 12.2 1.0
OG1 D:THR26 4.8 14.0 1.0
N D:ARG20 4.8 12.7 1.0
C D:VAL19 4.9 13.5 1.0
OE2 D:GLU31 4.9 17.0 1.0

Reference:

O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein. The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation. J.Mol.Biol. V. 391 536 2009.
ISSN: ISSN 0022-2836
PubMed: 19501594
DOI: 10.1016/J.JMB.2009.06.004
Page generated: Tue Dec 15 05:57:11 2020

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