Atomistry » Cadmium » PDB 4qe1-5ai3 » 4zty
Atomistry »
  Cadmium »
    PDB 4qe1-5ai3 »
      4zty »

Cadmium in PDB 4zty: Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+

Enzymatic activity of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+

All present enzymatic activity of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+:
2.1.1.14;

Protein crystallography data

The structure of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+, PDB code: 4zty was solved by R.W.Wheatley, K.K.Ng, M.Kapoor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.02 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.045, 95.198, 115.124, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ (pdb code 4zty). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+, PDB code: 4zty:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 1 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1000

b:28.3
occ:1.00
 NE2 A:HIS652 2.3 24.9 1.0
O A:HOH5805 2.5 25.4 1.0
OE2 A:GLU676 2.5 91.2 1.0
SG A:CYS654 2.5 37.8 1.0
SG A:CYS737 2.6 20.3 0.5
SG A:CYS737 2.6 16.7 0.5
CD2 A:HIS652 3.2 19.9 1.0
CD A:GLU676 3.3 70.4 1.0
CE1 A:HIS652 3.4 20.9 1.0
CB A:CYS737 3.4 18.7 0.5
CB A:CYS737 3.4 23.6 0.5
CG A:GLU676 3.5 43.0 1.0
CB A:CYS654 3.8 51.4 1.0
CD A:CD1002 3.8 33.4 1.0
CA A:CYS737 3.9 16.4 0.5
CA A:CYS737 3.9 14.6 0.5
CD A:CD1001 3.9 47.5 0.9
O A:ASP736 3.9 20.0 1.0
CA A:CYS654 4.0 33.7 1.0
CD A:CD1003 4.2 57.2 0.6
CG A:HIS652 4.4 25.6 1.0
ND1 A:HIS652 4.4 21.0 1.0
OE1 A:GLU676 4.5 84.4 1.0
N A:CYS654 4.7 21.9 1.0
O A:HOH5498 4.7 28.1 1.0
C A:ASP736 4.7 22.0 1.0
N A:CYS737 4.8 17.4 1.0
N A:GLY738 4.9 18.0 1.0
O A:HOH5419 4.9 24.8 1.0
O A:PHE653 4.9 22.4 1.0
C A:CYS737 5.0 18.4 1.0
O A:HOH5777 5.0 66.2 1.0
O A:HOH5603 5.0 33.9 1.0

Cadmium binding site 2 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 2 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:47.5
occ:0.90
 O A:HOH5684 2.4 44.9 1.0
O A:HOH5777 2.4 66.2 1.0
SG A:CYS654 2.5 37.8 1.0
O A:HOH5501 2.9 37.6 1.0
CB A:CYS654 3.5 51.4 1.0
CD A:CD1003 3.8 57.2 0.6
O A:HOH5498 3.9 28.1 1.0
CD A:CD1000 3.9 28.3 1.0
O A:HOH5805 4.1 25.4 1.0
OE2 A:GLU676 4.3 91.2 1.0
O A:HOH5603 4.5 33.9 1.0
O A:HOH5419 4.5 24.8 1.0
CD A:CD1002 4.6 33.4 1.0
SG A:CYS737 4.8 20.3 0.5
CA A:CYS654 4.9 33.7 1.0
O A:HOH5377 4.9 37.0 1.0

Cadmium binding site 3 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 3 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:33.4
occ:1.00
 NE2 A:HIS705 2.2 28.6 1.0
O A:HOH5419 2.4 24.8 1.0
SG A:CYS737 2.5 16.7 0.5
OE2 A:GLU676 2.6 91.2 1.0
O A:HOH5498 2.7 28.1 1.0
CE1 A:HIS705 2.8 26.6 1.0
SG A:CYS737 2.9 20.3 0.5
O A:HOH5493 3.0 53.3 1.0
CB A:CYS737 3.4 23.6 0.5
CB A:CYS737 3.4 18.7 0.5
CD2 A:HIS705 3.5 25.5 1.0
CD A:GLU676 3.6 70.4 1.0
CD A:CD1000 3.8 28.3 1.0
CD A:CD1003 4.0 57.2 0.6
OE1 A:GLU676 4.0 84.4 1.0
ND1 A:HIS705 4.1 36.2 1.0
O A:HOH5777 4.2 66.2 1.0
CG A:HIS705 4.4 27.8 1.0
CD A:CD1001 4.6 47.5 0.9
CD1 A:ILE704 4.6 18.6 1.0
O A:HOH5769 4.8 53.1 1.0
CG A:GLU676 4.8 43.0 1.0
CA A:CYS737 4.9 14.6 0.5
CA A:CYS737 4.9 16.4 0.5
O A:HOH5805 4.9 25.4 1.0

Cadmium binding site 4 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 4 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:57.2
occ:0.60
 O A:CYS654 2.4 54.2 1.0
O A:HOH5777 2.4 66.2 1.0
OE1 A:GLU676 2.4 84.4 1.0
O A:HOH5419 2.4 24.8 1.0
O A:HOH5794 2.4 28.9 1.0
OE2 A:GLU676 2.5 91.2 1.0
CD A:GLU676 2.6 70.4 1.0
CB A:CYS654 3.0 51.4 1.0
C A:CYS654 3.2 27.5 1.0
CA A:CYS654 3.4 33.7 1.0
SG A:CYS654 3.5 37.8 1.0
CD A:CD1001 3.8 47.5 0.9
CG A:GLU676 3.9 43.0 1.0
CD A:CD1002 4.0 33.4 1.0
CD A:CD1000 4.2 28.3 1.0
O A:HOH5493 4.2 53.3 1.0
N A:TYR655 4.4 26.1 1.0
O A:HOH5684 4.5 44.9 1.0
SG A:CYS737 4.6 16.7 0.5
CB A:GLU676 4.7 43.3 1.0
N A:CYS654 4.8 21.9 1.0

Cadmium binding site 5 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 5 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:46.2
occ:0.65
 NE2 A:HIS663 2.3 49.4 1.0
O A:HOH5800 2.4 51.9 1.0
O A:HOH5801 2.4 55.2 1.0
OE2 A:GLU691 2.4 30.8 1.0
OE1 A:GLU691 2.5 42.9 1.0
CD A:GLU691 2.8 34.8 1.0
CE1 A:HIS663 3.2 55.2 1.0
CD2 A:HIS663 3.3 62.0 1.0
O A:HOH5650 3.8 50.5 1.0
ND1 A:HIS663 4.3 94.1 1.0
CG A:GLU691 4.3 26.7 1.0
CG A:HIS663 4.4 83.0 1.0
O A:HOH5723 4.5 33.6 1.0
O A:HOH5575 4.5 41.4 1.0
O A:HOH5393 4.9 39.6 1.0
CB A:GLU691 5.0 25.7 1.0

Cadmium binding site 6 out of 6 in 4zty

Go back to Cadmium Binding Sites List in 4zty
Cadmium binding site 6 out of 6 in the Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Neurospora Crassa Cobalamin-Independent Methionine Synthase Complexed with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:68.6
occ:0.38
 OE1 A:GLU426 2.5 69.9 1.0
CD A:GLU426 3.6 46.0 1.0
O A:HOH5245 3.7 47.4 1.0
O A:HOH5645 4.1 44.2 1.0
O A:HOH5707 4.3 43.0 1.0
O A:HOH5763 4.3 48.5 1.0
NZ A:LYS429 4.3 58.0 1.0
OE2 A:GLU426 4.5 64.9 1.0
CG A:GLU426 4.5 41.4 1.0
CB A:GLU426 4.7 56.5 1.0

Reference:

R.W.Wheatley, K.K.Ng, M.Kapoor. Fungal Cobalamin-Independent Methionine Synthase: Insights From the Model Organism, Neurospora Crassa. Arch.Biochem.Biophys. V. 590 125 2015.
ISSN: ESSN 1096-0384
PubMed: 26657067
DOI: 10.1016/J.ABB.2015.11.037
Page generated: Thu Jul 10 14:07:31 2025

Last articles

Fe in 3UH5
Fe in 3UGZ
Fe in 3UH3
Fe in 3UGY
Fe in 3UFW
Fe in 3UFV
Fe in 3UGW
Fe in 3UFK
Fe in 3UFU
Fe in 3UFT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy