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Sodium in PDB 1zkp: 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease

Protein crystallography data

The structure of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease, PDB code: 1zkp was solved by J.S.Brunzelle, G.Minasov, L.Shuvalova, F.R.Collart, W.F.Anderson, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.375, 91.190, 78.466, 90.00, 115.31, 90.00
R / Rfree (%) 14.7 / 18

Other elements in 1zkp:

The structure of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease (pdb code 1zkp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease, PDB code: 1zkp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1zkp

Go back to Sodium Binding Sites List in 1zkp
Sodium binding site 1 out of 4 in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na247

b:26.3
occ:1.00
O A:HOH414 2.3 32.1 1.0
O A:HOH415 2.3 37.7 1.0
O A:HOH274 2.4 15.6 1.0
O A:HOH358 2.4 31.9 1.0
O A:HOH295 2.5 23.5 1.0
O A:HOH319 2.6 27.9 1.0
NH1 A:ARG30 3.9 20.9 1.0
O A:HOH413 4.0 42.8 1.0
O A:HOH416 4.1 31.4 1.0
O A:GLY28 4.2 17.7 1.0
OD1 A:ASP53 4.5 19.2 1.0
O A:ASP51 4.5 14.6 1.0
OD1 A:ASP51 4.5 22.2 1.0
OD2 A:ASP53 4.5 16.7 1.0
O A:HOH401 4.7 31.1 1.0
O A:HOH402 4.8 35.4 1.0
CA A:ASP51 4.8 14.9 1.0
CG A:ASP53 5.0 15.8 1.0

Sodium binding site 2 out of 4 in 1zkp

Go back to Sodium Binding Sites List in 1zkp
Sodium binding site 2 out of 4 in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na248

b:25.5
occ:1.00
O B:HOH274 2.2 17.2 1.0
O B:HOH466 2.4 34.3 1.0
O B:HOH469 2.4 32.6 1.0
O B:HOH346 2.4 23.4 1.0
O B:HOH437 2.9 34.0 1.0
O B:HOH314 2.9 26.5 1.0
NA B:NA249 3.7 22.7 1.0
OD2 B:ASP53 3.9 19.7 1.0
NH1 B:ARG30 4.0 16.7 1.0
OD1 B:ASP53 4.1 17.0 1.0
O B:ASP51 4.3 13.7 1.0
O B:GLY28 4.4 15.6 1.0
CG B:ASP53 4.4 16.2 1.0
O B:HOH265 4.6 19.1 1.0
CA B:ASP51 4.7 13.9 1.0
O B:HOH551 4.7 41.0 1.0
OD1 B:ASP51 4.7 19.8 1.0
C B:ASP51 4.9 13.1 1.0

Sodium binding site 3 out of 4 in 1zkp

Go back to Sodium Binding Sites List in 1zkp
Sodium binding site 3 out of 4 in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na249

b:22.7
occ:1.00
O B:HOH469 2.3 32.6 1.0
O B:HOH265 2.4 19.1 1.0
O B:HOH346 2.4 23.4 1.0
NA B:NA248 3.7 25.5 1.0
O B:HOH438 3.7 26.6 1.0
O B:HOH403 3.9 21.9 1.0
OD2 B:ASP53 4.3 19.7 1.0
O B:GLY28 4.5 15.6 1.0
OD1 B:ASP53 4.6 17.0 1.0
CG B:ASP53 4.7 16.2 1.0
O B:HOH274 4.7 17.2 1.0
O B:HOH588 5.0 40.4 1.0

Sodium binding site 4 out of 4 in 1zkp

Go back to Sodium Binding Sites List in 1zkp
Sodium binding site 4 out of 4 in the 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na247

b:21.9
occ:1.00
O C:HOH388 2.4 26.4 1.0
O C:HOH439 2.4 29.4 1.0
O C:HOH315 2.4 22.1 1.0
O C:HOH265 2.4 14.7 1.0
O C:HOH327 2.4 25.2 1.0
O C:HOH270 2.5 21.9 1.0
O C:HOH502 3.3 30.9 1.0
NH1 C:ARG30 3.8 19.8 1.0
O C:HOH297 4.2 25.9 1.0
O C:GLY28 4.3 15.0 1.0
O C:HOH371 4.3 30.2 1.0
OD1 C:ASP53 4.4 18.6 1.0
O C:HOH403 4.4 27.1 1.0
O C:ASP51 4.5 14.6 1.0
O C:HOH390 4.5 27.3 1.0
OD2 C:ASP53 4.5 16.3 1.0
OD1 C:ASP51 4.5 18.8 1.0
O C:HOH427 4.6 32.3 1.0
CA C:ASP51 4.9 14.9 1.0
CG C:ASP53 4.9 15.2 1.0

Reference:

J.S.Brunzelle, G.Minasov, L.Shuvalova, F.R.Collart, W.F.Anderson, Midwest Center For Structural Genomics (Mcsg). 1.5A Resolution Crystal Structure of A Metallo Beta Lactamase Family Protein, the Elac Homolgue of Bacillus Anthracis, A Putative Ribonuclease To Be Published.
Page generated: Mon Oct 7 01:42:40 2024

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