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Zinc in PDB 2rjp: Crystal Structure of ADAMTS4 with Inhibitor Bound

Enzymatic activity of Crystal Structure of ADAMTS4 with Inhibitor Bound

All present enzymatic activity of Crystal Structure of ADAMTS4 with Inhibitor Bound:
3.4.24.82;

Protein crystallography data

The structure of Crystal Structure of ADAMTS4 with Inhibitor Bound, PDB code: 2rjp was solved by L.Mosyak, M.Stahl, W.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.566, 82.618, 99.326, 90.00, 90.63, 90.00
R / Rfree (%) 20.6 / 26.7

Other elements in 2rjp:

The structure of Crystal Structure of ADAMTS4 with Inhibitor Bound also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of ADAMTS4 with Inhibitor Bound (pdb code 2rjp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of ADAMTS4 with Inhibitor Bound, PDB code: 2rjp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2rjp

Go back to Zinc Binding Sites List in 2rjp
Zinc binding site 1 out of 4 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:37.0
occ:1.00
O1 A:886510 2.0 59.2 1.0
NE2 A:HIS371 2.0 40.2 1.0
NE2 A:HIS361 2.1 41.9 1.0
NE2 A:HIS365 2.1 39.7 1.0
C5 A:886510 2.5 59.4 1.0
O2 A:886510 2.5 58.7 1.0
CE1 A:HIS371 2.9 40.2 1.0
CE1 A:HIS361 3.0 41.8 1.0
CD2 A:HIS365 3.0 41.2 1.0
CD2 A:HIS371 3.0 40.4 1.0
CD2 A:HIS361 3.1 42.1 1.0
CE1 A:HIS365 3.1 39.9 1.0
C4 A:886510 4.0 60.9 1.0
ND1 A:HIS371 4.0 40.2 1.0
CG A:HIS371 4.1 40.8 1.0
ND1 A:HIS361 4.1 42.9 1.0
CG A:HIS365 4.2 42.2 1.0
ND1 A:HIS365 4.2 40.6 1.0
CG A:HIS361 4.2 43.4 1.0
N1 A:886510 4.3 62.0 1.0
C6 A:886510 4.8 62.4 1.0
CE A:MET391 4.8 47.5 1.0
C7 A:886510 4.9 62.0 1.0
C2 A:886510 4.9 61.4 1.0
C11 A:886510 4.9 62.0 1.0
NE2 A:GLN362 5.0 45.1 1.0

Zinc binding site 2 out of 4 in 2rjp

Go back to Zinc Binding Sites List in 2rjp
Zinc binding site 2 out of 4 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


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 ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:34.0
occ:1.00
O1 B:886510 1.9 43.5 1.0
NE2 B:HIS361 2.0 46.7 1.0
NE2 B:HIS365 2.1 44.5 1.0
NE2 B:HIS371 2.1 47.2 1.0
C5 B:886510 2.7 45.4 1.0
CE1 B:HIS361 2.9 47.0 1.0
O2 B:886510 2.9 46.3 1.0
CD2 B:HIS361 3.0 46.3 1.0
CD2 B:HIS365 3.0 44.2 1.0
CE1 B:HIS365 3.0 45.0 1.0
CE1 B:HIS371 3.1 46.8 1.0
CD2 B:HIS371 3.1 46.6 1.0
ND1 B:HIS361 4.0 47.1 1.0
CG B:HIS361 4.1 46.6 1.0
ND1 B:HIS365 4.1 45.0 1.0
C4 B:886510 4.2 46.2 1.0
CG B:HIS365 4.2 45.2 1.0
ND1 B:HIS371 4.2 46.2 1.0
CG B:HIS371 4.3 45.7 1.0
N1 B:886510 4.4 46.5 1.0
CE B:MET391 4.5 44.0 1.0
C7 B:886510 4.7 45.8 1.0
C6 B:886510 4.8 45.9 1.0
O B:HOH511 4.9 37.3 1.0
O B:HOH536 4.9 42.0 1.0
C8 B:886510 4.9 46.1 1.0
O B:ALA392 5.0 48.1 1.0
O B:HOH532 5.0 43.0 1.0

Zinc binding site 3 out of 4 in 2rjp

Go back to Zinc Binding Sites List in 2rjp
Zinc binding site 3 out of 4 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:38.1
occ:1.00
O1 C:886510 1.8 47.3 1.0
NE2 C:HIS361 2.0 38.6 1.0
NE2 C:HIS371 2.1 41.9 1.0
NE2 C:HIS365 2.2 35.2 1.0
C5 C:886510 2.6 48.0 1.0
O2 C:886510 2.9 49.2 1.0
CD2 C:HIS361 2.9 38.2 1.0
CE1 C:HIS361 3.0 38.7 1.0
CD2 C:HIS365 3.0 36.0 1.0
CE1 C:HIS371 3.0 41.4 1.0
CD2 C:HIS371 3.1 42.0 1.0
CE1 C:HIS365 3.3 36.0 1.0
C4 C:886510 4.0 48.1 1.0
ND1 C:HIS361 4.1 39.0 1.0
CG C:HIS361 4.1 38.8 1.0
ND1 C:HIS371 4.2 41.5 1.0
CG C:HIS371 4.2 41.6 1.0
CG C:HIS365 4.2 37.0 1.0
N1 C:886510 4.3 48.9 1.0
ND1 C:HIS365 4.3 36.4 1.0
C7 C:886510 4.4 49.8 1.0
CE C:MET391 4.6 47.7 1.0
C8 C:886510 4.6 50.3 1.0
NE2 C:GLN362 4.7 42.4 1.0
C6 C:886510 4.8 50.4 1.0
C3 C:886510 4.8 47.6 1.0

Zinc binding site 4 out of 4 in 2rjp

Go back to Zinc Binding Sites List in 2rjp
Zinc binding site 4 out of 4 in the Crystal Structure of ADAMTS4 with Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of ADAMTS4 with Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:48.1
occ:1.00
O1 D:886510 1.8 66.4 1.0
NE2 D:HIS365 2.1 37.1 1.0
NE2 D:HIS371 2.1 40.8 1.0
NE2 D:HIS361 2.1 37.5 1.0
C5 D:886510 2.7 67.2 1.0
CE1 D:HIS371 2.9 40.7 1.0
CD2 D:HIS361 2.9 36.8 1.0
CD2 D:HIS365 3.0 36.8 1.0
O2 D:886510 3.0 67.4 1.0
CE1 D:HIS365 3.1 37.6 1.0
CD2 D:HIS371 3.2 40.6 1.0
CE1 D:HIS361 3.2 37.2 1.0
ND1 D:HIS371 4.0 40.5 1.0
C4 D:886510 4.1 67.4 1.0
CG D:HIS361 4.1 37.4 1.0
CG D:HIS365 4.2 37.1 1.0
CG D:HIS371 4.2 40.3 1.0
ND1 D:HIS365 4.2 36.9 1.0
ND1 D:HIS361 4.2 37.3 1.0
N1 D:886510 4.3 67.5 1.0
C7 D:886510 4.4 66.0 1.0
CE D:MET391 4.5 43.1 1.0
C8 D:886510 4.6 66.3 1.0
C3 D:886510 4.7 67.4 1.0
C6 D:886510 4.7 66.5 1.0

Reference:

L.Mosyak, K.Georgiadis, T.Shane, K.Svenson, T.Hebert, T.Mcdonagh, S.Mackie, S.Olland, L.Lin, X.Zhong, R.Kriz, E.L.Reifenberg, L.A.Collins-Racie, C.Corcoran, B.Freeman, R.Zollner, T.Marvell, M.Vera, P.E.Sum, E.R.Lavallie, M.Stahl, W.Somers. Crystal Structures of the Two Major Aggrecan Degrading Enzymes, ADAMTS4 and ADAMTS5. Protein Sci. V. 17 16 2008.
ISSN: ISSN 0961-8368
PubMed: 18042673
DOI: 10.1110/PS.073287008
Page generated: Wed Dec 16 03:52:19 2020

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