Atomistry » Nickel » PDB 1t6u-1xmk » 1uwv
Atomistry »
  Nickel »
    PDB 1t6u-1xmk »
      1uwv »

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: Wed Oct 9 16:29:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy