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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

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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

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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

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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

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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: Sat Dec 12 08:26:09 2020

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