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Zinc in PDB 3edh: Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso

Enzymatic activity of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso

All present enzymatic activity of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso:
3.4.24.19;

Protein crystallography data

The structure of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso, PDB code: 3edh was solved by A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.99 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.499, 59.093, 69.451, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso (pdb code 3edh). 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 Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso, PDB code: 3edh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3edh

Go back to Zinc Binding Sites List in 3edh
Zinc binding site 1 out of 2 in the Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso


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 Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:7.0
occ:1.00
O A:DMS214 1.8 12.3 0.3
O A:DMS214 1.9 8.9 0.3
NE2 A:HIS92 2.0 6.4 1.0
NE2 A:HIS102 2.0 6.2 1.0
NE2 A:HIS96 2.1 6.1 1.0
S A:DMS214 3.0 12.3 0.3
CE1 A:HIS92 3.0 7.0 1.0
CE1 A:HIS102 3.0 6.7 1.0
CE1 A:HIS96 3.0 6.0 1.0
CD2 A:HIS102 3.0 6.1 1.0
CD2 A:HIS92 3.0 6.5 1.0
CD2 A:HIS96 3.1 5.5 1.0
S A:DMS214 3.2 16.3 0.3
C1 A:DMS214 3.2 11.3 0.3
C2 A:DMS214 3.4 14.4 0.3
O A:HOH306 3.9 18.0 1.0
C1 A:DMS214 4.0 9.1 0.3
C2 A:DMS214 4.1 7.5 0.3
ND1 A:HIS102 4.1 6.8 1.0
ND1 A:HIS92 4.1 6.3 1.0
ND1 A:HIS96 4.2 6.2 1.0
O A:HOH297 4.2 20.2 1.0
CG A:HIS102 4.2 6.2 1.0
CG A:HIS92 4.2 5.8 1.0
CG A:HIS96 4.2 5.8 1.0
OE2 A:GLU93 4.3 14.9 1.0
O A:HOH261 4.6 14.4 1.0
CE A:MET147 4.7 8.6 1.0
O A:HOH280 4.7 16.3 1.0
SG A:CYS64 4.8 15.5 0.5
O A:HOH604 4.8 32.2 1.0
O A:HOH314 4.8 17.2 1.0
OE1 A:GLU93 4.8 12.7 1.0
CD A:GLU93 4.9 9.3 1.0

Zinc binding site 2 out of 2 in 3edh

Go back to Zinc Binding Sites List in 3edh
Zinc binding site 2 out of 2 in the Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso


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 Bone Morphogenetic Protein 1 Protease Domain in Complex with Partially Bound Dmso within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn211

b:5.2
occ:0.50
O A:ACE201 2.3 7.5 1.0
O A:HOH221 2.4 7.9 1.0
NE2 A:GLN189 2.4 4.9 1.0
O A:HOH228 2.4 8.8 1.0
O A:HOH224 2.4 7.3 1.0
OE1 A:GLU103 2.4 8.1 1.0
OE2 A:GLU103 2.5 6.2 1.0
CD A:GLU103 2.8 6.8 1.0
C A:ACE201 3.4 6.8 1.0
CD A:GLN189 3.5 7.1 1.0
OE1 A:GLN189 3.8 10.6 1.0
N A:ALA1 3.9 6.5 1.0
O A:HOH219 4.0 8.0 1.0
CB A:ASP142 4.2 7.0 1.0
NH1 A:ARG106 4.2 7.6 1.0
CG A:GLU103 4.4 6.9 1.0
CH3 A:ACE201 4.5 3.4 1.0
O A:HOH225 4.5 8.6 1.0
OD1 A:ASP186 4.7 7.8 1.0
CG A:GLN189 4.7 7.4 1.0
OG A:SER145 4.8 6.5 1.0
OD2 A:ASP142 4.8 7.0 1.0
N A:ASP142 4.9 6.6 1.0
O A:THR140 4.9 8.3 1.0
CB A:GLN189 4.9 7.1 1.0
CD A:ARG106 4.9 6.9 1.0
CB A:SER145 4.9 6.4 1.0
CE2 A:PHE100 5.0 10.0 0.7

Reference:

A.Mac Sweeney, S.G.Parrado, D.Vinzenz, A.Bernardi, A.Hein, U.Bodendorf, P.Erbel, C.Logel, B.Gerhartz. Structural Basis For the Substrate Specificity of Bone Morphogenetic Protein 1/Tolloid-Like Metalloproteases To Be Published.
Page generated: Wed Dec 16 04:15:40 2020

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