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Nickel in PDB 1uwv: Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase

Protein crystallography data

The structure of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase, PDB code: 1uwv was solved by T.T.Lee, S.Agarwalla, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.938, 99.448, 58.519, 90.00, 100.57, 90.00
R / Rfree (%) 18.6 / 22.7

Other elements in 1uwv:

The structure of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase (pdb code 1uwv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase, PDB code: 1uwv:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1uwv

Go back to Nickel Binding Sites List in 1uwv
Nickel binding site 1 out of 2 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1433

b:36.9
occ:1.00
O A:HOH2116 1.8 28.6 1.0
O A:HOH2117 2.0 41.8 1.0
NE2 A:HIS114 2.1 18.2 1.0
O A:HOH2050 2.6 41.6 1.0
CE1 A:HIS114 3.1 13.7 1.0
CD2 A:HIS114 3.1 15.4 1.0
O A:ILE408 3.6 16.2 1.0
ND1 A:HIS114 4.2 13.8 1.0
CG A:HIS114 4.2 14.6 1.0
OD1 A:ASP115 4.5 27.4 1.0
C A:ILE408 4.8 16.0 1.0

Nickel binding site 2 out of 2 in 1uwv

Go back to Nickel Binding Sites List in 1uwv
Nickel binding site 2 out of 2 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1434

b:47.0
occ:1.00
OE1 A:GLU193 2.0 26.5 1.0
NE2 A:HIS191 2.1 31.6 1.0
CL A:CL1436 2.5 62.1 1.0
CE1 A:HIS191 2.7 30.6 1.0
CD A:GLU193 2.8 24.0 1.0
NH1 A:ARG132 3.0 34.7 1.0
OE2 A:GLU193 3.0 29.4 1.0
CD2 A:HIS191 3.3 32.4 1.0
ND1 A:HIS191 3.9 28.9 1.0
O1 A:PO41435 3.9 51.6 1.0
CZ A:ARG132 3.9 32.4 1.0
CG A:HIS191 4.2 20.4 1.0
CG A:GLU193 4.2 19.9 1.0
CD A:ARG132 4.3 24.6 1.0
NE A:ARG132 4.4 32.4 1.0
CB A:ARG206 4.7 10.2 1.0
NH2 A:ARG132 4.8 32.9 1.0
O2 A:PO41435 4.9 49.5 1.0
P A:PO41435 5.0 49.0 1.0

Reference:

T.T.Lee, S.Agarwalla, R.M.Stroud. Crystal Structure of Ruma, An Iron-Sulfur Cluster Containing E. Coli Ribosomal Rna 5-Methyluridine Methyltransferase. Structure V. 12 397 2004.
ISSN: ISSN 0969-2126
PubMed: 15016356
DOI: 10.1016/J.STR.2004.02.009
Page generated: Thu Oct 29 06:15:58 2020
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