Zinc in PDB 7dmr: Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution

Enzymatic activity of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution

All present enzymatic activity of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution, PDB code: 7dmr was solved by P.K.Singh, C.Rani, P.Sharma, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.61 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.240, 85.310, 98.930, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.3

Other elements in 7dmr:

The structure of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution also contains other interesting chemical elements:

Potassium (K) 1 atom
Iron (Fe) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution (pdb code 7dmr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution, PDB code: 7dmr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7dmr

Go back to Zinc Binding Sites List in 7dmr
Zinc binding site 1 out of 2 in the Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:35.9
occ:1.00
ND1 A:HIS558 2.0 26.4 1.0
ND1 A:HIS222 2.0 38.5 1.0
O A:HOH1079 2.2 43.0 1.0
CE1 A:HIS558 2.9 27.8 1.0
CE1 A:HIS222 2.9 41.1 1.0
CG A:HIS222 3.0 36.5 1.0
CG A:HIS558 3.1 25.9 1.0
CB A:HIS222 3.4 32.3 1.0
CB A:HIS558 3.5 24.6 1.0
O A:HOH898 3.6 25.7 1.0
NE2 A:HIS558 4.0 24.5 1.0
NE2 A:HIS222 4.1 41.4 1.0
CD2 A:HIS222 4.1 38.1 1.0
CD2 A:HIS558 4.1 26.1 1.0
O A:HOH730 4.5 31.4 1.0
O A:HIS222 4.6 33.9 1.0
CA A:HIS222 4.8 32.1 1.0
OD2 A:ASP393 4.9 30.2 1.0

Zinc binding site 2 out of 2 in 7dmr

Go back to Zinc Binding Sites List in 7dmr
Zinc binding site 2 out of 2 in the Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:59.3
occ:0.50
OE1 A:GLU130 1.9 54.9 1.0
O A:HOH752 2.3 49.3 1.0
ND1 A:HIS426 2.3 43.4 1.0
CD A:GLU130 2.5 54.4 1.0
OE2 A:GLU130 2.5 53.1 1.0
CG A:HIS426 3.2 42.0 1.0
CA A:HIS426 3.3 40.7 1.0
CB A:HIS426 3.4 40.6 1.0
CE1 A:HIS426 3.4 43.3 1.0
CG A:GLU130 3.9 54.9 1.0
N A:LYS427 4.1 37.7 1.0
O A:THR425 4.2 49.9 1.0
CE A:LYS427 4.2 55.5 1.0
C A:HIS426 4.2 37.8 1.0
N A:HIS426 4.4 44.2 1.0
CD2 A:HIS426 4.4 41.5 1.0
NE2 A:HIS426 4.5 40.0 1.0
CB A:GLU130 4.6 52.7 1.0
C A:THR425 4.6 45.8 1.0
NZ A:LYS427 4.9 57.0 1.0

Reference:

P.K.Singh, C.Rani, P.Sharma, S.Shrama, T.P.Singh. Crystal Structure of Potassium Induced Heme Modification in Yak Lactoperoxidase at 2.20 A Resolution To Be Published.
Page generated: Wed Dec 16 13:44:13 2020

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