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Calcium in PDB 3ohl: Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide

Enzymatic activity of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide

All present enzymatic activity of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide:
3.4.24.17;

Protein crystallography data

The structure of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide, PDB code: 3ohl was solved by T.Kowatz, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.31 / 2.36
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.964, 120.512, 46.627, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 28.3

Other elements in 3ohl:

The structure of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide (pdb code 3ohl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide, PDB code: 3ohl:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ohl

Go back to Calcium Binding Sites List in 3ohl
Calcium binding site 1 out of 3 in the Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:46.7
occ:1.00
 O A:ASP182 2.3 42.4 1.0
OD2 A:ASP107 2.3 45.6 1.0
OD1 A:ASP182 2.3 39.2 1.0
O A:GLU184 2.5 41.2 1.0
O A:HOH23 2.7 41.1 1.0
OD1 A:ASP107 2.9 47.4 1.0
CG A:ASP107 2.9 46.2 1.0
C A:ASP182 3.1 42.1 1.0
CG A:ASP182 3.4 39.2 1.0
CA A:ASP182 3.6 39.8 1.0
C A:GLU184 3.7 47.4 1.0
OG1 A:THR105 3.7 38.6 1.0
CB A:ASP182 3.9 38.8 1.0
CD1 A:TRP186 4.0 44.3 1.0
N A:ASP183 4.2 42.4 1.0
N A:GLU184 4.3 44.7 1.0
CB A:ASP107 4.4 45.7 1.0
CA A:GLN185 4.5 55.7 1.0
OD2 A:ASP182 4.5 39.4 1.0
C A:ASP183 4.5 46.4 1.0
NE1 A:TRP186 4.5 43.0 1.0
N A:GLN185 4.5 53.1 1.0
CA A:ASP183 4.6 44.9 1.0
N A:TRP186 4.6 51.6 1.0
OE1 A:GLN185 4.7 71.2 1.0
CA A:GLU184 4.7 46.1 1.0
N A:ASP182 4.9 40.3 1.0
CD A:PRO106 4.9 41.8 1.0
O A:ASP181 4.9 42.3 1.0
CG A:TRP186 5.0 45.5 1.0

Calcium binding site 2 out of 3 in 3ohl

Go back to Calcium Binding Sites List in 3ohl
Calcium binding site 2 out of 3 in the Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:42.2
occ:1.00
 O A:HOH9 2.2 35.7 1.0
OD1 A:ASP177 2.3 40.4 1.0
O A:GLY173 2.3 44.2 1.0
O A:ASP141 2.3 45.0 1.0
O A:ASN175 2.3 43.4 1.0
O A:HOH251 2.6 40.5 1.0
CG A:ASP177 3.2 37.9 1.0
C A:ASP141 3.5 47.8 1.0
C A:ASN175 3.5 43.7 1.0
C A:GLY173 3.5 46.1 1.0
OD2 A:ASP177 3.7 35.5 1.0
C A:ILE174 4.0 44.8 1.0
N A:ASP177 4.1 38.7 1.0
O A:ALA140 4.1 49.6 1.0
N A:ASN175 4.1 45.8 1.0
O A:ILE174 4.2 42.9 1.0
CA A:ASP141 4.2 51.8 1.0
N A:GLY176 4.4 42.6 1.0
N A:ILE174 4.4 44.9 1.0
N A:GLY173 4.4 48.1 1.0
CA A:ILE174 4.4 45.1 1.0
C A:GLY176 4.4 39.9 1.0
CA A:GLY176 4.4 42.2 1.0
CA A:ASN175 4.4 44.4 1.0
O A:GLY171 4.4 43.3 1.0
CB A:ASP177 4.4 36.0 1.0
CA A:GLY173 4.5 47.6 1.0
N A:ILE142 4.5 47.3 1.0
CA A:ASP177 4.6 37.4 1.0
N A:MET143 4.7 42.1 1.0
C A:PRO172 4.8 47.6 1.0
CA A:ILE142 4.8 45.0 1.0
CG A:MET143 4.8 44.5 1.0
O A:HOH21 4.8 38.3 1.0
CH2 A:TRP92 5.0 58.1 1.0

Calcium binding site 3 out of 3 in 3ohl

Go back to Calcium Binding Sites List in 3ohl
Calcium binding site 3 out of 3 in the Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Stromelysin-1 in Complex with N-Hydroxy-2-(4- Methoxy-N-(Pyridine-3-Ylmethyl)Phenylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:47.6
occ:1.00
 O A:VAL163 2.3 50.0 1.0
OE2 A:GLU184 2.3 45.1 1.0
O A:GLY159 2.3 52.9 1.0
OD2 A:ASP181 2.3 45.1 1.0
O A:GLY161 2.3 58.2 1.0
OD1 A:ASP158 2.3 49.2 1.0
C A:VAL163 3.4 53.0 1.0
CG A:ASP181 3.4 43.0 1.0
CD A:GLU184 3.5 46.4 1.0
C A:GLY161 3.5 63.0 1.0
C A:GLY159 3.6 56.5 1.0
CG A:ASP158 3.6 51.9 1.0
N A:VAL163 3.9 60.4 1.0
CB A:ASP181 4.0 42.3 1.0
N A:GLY161 4.0 60.6 1.0
CA A:VAL163 4.1 56.4 1.0
N A:GLY159 4.1 53.4 1.0
C A:PRO160 4.2 61.6 1.0
C A:ASP158 4.2 53.0 1.0
N A:ASP158 4.2 48.1 1.0
OE1 A:GLU184 4.2 47.4 1.0
OD2 A:ASP158 4.3 53.7 1.0
C A:ASN162 4.3 63.8 1.0
N A:LEU164 4.3 51.2 1.0
CA A:GLY161 4.4 63.0 1.0
OD1 A:ASP181 4.4 42.2 1.0
CA A:GLY159 4.5 55.1 1.0
N A:PRO160 4.5 58.1 1.0
CA A:PRO160 4.5 59.5 1.0
CG A:GLU184 4.5 45.0 1.0
N A:ASN162 4.5 66.6 1.0
CA A:ASP158 4.6 51.9 1.0
CA A:LEU164 4.6 48.6 1.0
O A:ASP158 4.6 53.4 1.0
CB A:VAL163 4.6 55.8 1.0
O A:PRO160 4.6 62.8 1.0
CB A:ASP158 4.6 52.8 1.0
CB A:ASN162 4.7 70.7 1.0
CA A:ASN162 4.7 67.7 1.0
O A:ASN162 4.8 64.6 1.0

Reference:

T.Kowatz, J.H.Naismith. Non-Resonance Raman Difference Spectroscopy As A Tool to Probe Enthalpy-Entropy Compensation and the Interfacial Mobility Model To Be Published.
Page generated: Sat Jul 13 15:18:19 2024

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