Atomistry » Cadmium » PDB 1qvg-1vqo » 1rzm
Atomistry »
  Cadmium »
    PDB 1qvg-1vqo »
      1rzm »

Cadmium in PDB 1rzm: Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P

Enzymatic activity of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P

All present enzymatic activity of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P:
2.5.1.54;

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P, PDB code: 1rzm was solved by I.A.Shumilin, R.Bauerle, J.Wu, R.W.Woodard, R.H.Kretsinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.581, 144.215, 141.057, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P (pdb code 1rzm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P, PDB code: 1rzm:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1rzm

Go back to Cadmium Binding Sites List in 1rzm
Cadmium binding site 1 out of 3 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd8001

b:46.1
occ:1.00
 NE2 A:HIS272 2.4 34.2 1.0
OD2 A:ASP309 2.4 53.0 1.0
OE2 A:GLU298 2.5 32.6 1.0
SG A:CYS102 2.7 32.9 1.0
OE1 A:GLU298 3.0 27.5 1.0
CD A:GLU298 3.1 30.5 1.0
CE1 A:HIS272 3.2 32.9 1.0
CD2 A:HIS272 3.3 29.4 1.0
CG A:ASP309 3.4 55.1 1.0
O A:HOH8055 3.4 48.8 1.0
CB A:CYS102 3.6 24.8 1.0
O2 A:E4P8003 3.7 77.7 1.0
CB A:ASP309 3.8 55.6 1.0
O1 A:PEP8002 3.9 32.3 1.0
NE2 A:GLN312 4.0 39.0 1.0
CA A:CYS102 4.2 24.9 1.0
NZ A:LYS131 4.2 41.6 1.0
C1 A:PEP8002 4.3 31.4 1.0
ND1 A:HIS272 4.3 34.4 1.0
CG A:HIS272 4.4 31.5 1.0
NH2 A:ARG126 4.4 32.1 1.0
OD1 A:ASP309 4.5 51.4 1.0
CG A:GLU298 4.5 31.1 1.0
C2 A:PEP8002 4.5 29.4 1.0
C3 A:PEP8002 4.7 30.6 1.0
C A:CYS102 4.9 26.5 1.0
C2 A:E4P8003 4.9 76.7 1.0
O2' A:PEP8002 4.9 30.7 1.0
CE A:LYS131 5.0 41.0 1.0

Cadmium binding site 2 out of 3 in 1rzm

Go back to Cadmium Binding Sites List in 1rzm
Cadmium binding site 2 out of 3 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9001

b:43.5
occ:1.00
 NE2 B:HIS272 2.4 37.6 1.0
OE2 B:GLU298 2.5 30.1 1.0
OD2 B:ASP309 2.5 52.5 1.0
SG B:CYS102 2.7 35.8 1.0
O1 B:E4P9003 2.9 81.3 1.0
OE1 B:GLU298 3.0 29.2 1.0
CD B:GLU298 3.1 26.4 1.0
C1 B:E4P9003 3.2 76.6 1.0
CE1 B:HIS272 3.2 35.2 1.0
CD2 B:HIS272 3.3 34.2 1.0
CG B:ASP309 3.5 55.1 1.0
CB B:CYS102 3.5 33.4 1.0
CB B:ASP309 3.8 55.5 1.0
NE2 B:GLN312 3.9 42.4 1.0
CA B:CYS102 4.1 32.3 1.0
ND1 B:HIS272 4.3 39.8 1.0
O1 B:PEP9002 4.4 33.1 1.0
CG B:HIS272 4.4 38.6 1.0
NH2 B:ARG126 4.5 37.7 1.0
C1 B:PEP9002 4.5 31.3 1.0
C2 B:E4P9003 4.5 73.8 1.0
CG B:GLU298 4.5 29.4 1.0
NZ B:LYS131 4.6 31.5 1.0
OD1 B:ASP309 4.6 53.4 1.0
C2 B:PEP9002 4.7 32.0 1.0
C B:CYS102 4.8 32.0 1.0
O B:CYS102 4.8 36.5 1.0
C3 B:E4P9003 4.9 70.5 1.0
O2 B:E4P9003 4.9 74.8 1.0
O2' B:PEP9002 4.9 29.5 1.0
C3 B:PEP9002 5.0 29.5 1.0
CD B:GLN312 5.0 41.7 1.0

Cadmium binding site 3 out of 3 in 1rzm

Go back to Cadmium Binding Sites List in 1rzm
Cadmium binding site 3 out of 3 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahps) From Thermotoga Maritima Complexed with CD2+, Pep and E4P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9009

b:35.8
occ:1.00
 NE2 B:HIS115 2.2 34.0 1.0
OE2 B:GLU119 2.4 39.1 1.0
OE1 B:GLU119 2.9 32.5 1.0
CD B:GLU119 3.0 36.1 1.0
CE1 B:HIS115 3.1 39.4 1.0
CD2 B:HIS115 3.3 31.0 1.0
ND1 B:HIS115 4.3 38.4 1.0
CG B:HIS115 4.4 36.1 1.0
CG B:GLU119 4.5 37.2 1.0
O B:HOH9063 4.6 40.9 1.0

Reference:

I.A.Shumilin, R.Bauerle, J.Wu, R.W.Woodard, R.H.Kretsinger. Crystal Structure of the Reaction Complex of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Thermotoga Maritima Refines the Catalytic Mechanism and Indicates A New Mechanism of Allosteric Regulation. J.Mol.Biol. V. 341 455 2004.
ISSN: ISSN 0022-2836
PubMed: 15276836
DOI: 10.1016/J.JMB.2004.05.077
Page generated: Fri Jul 19 14:12:50 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