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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: Sat Dec 12 08:12:37 2020

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