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Zinc in PDB 8orl: Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56

Enzymatic activity of Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56

All present enzymatic activity of Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56, PDB code: 8orl was solved by M.Rees, M.Gautel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.39 / 1.43
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.348, 89.862, 98.309, 90, 90, 90
R / Rfree (%) 15.9 / 19.4

Other elements in 8orl:

The structure of Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56 (pdb code 8orl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56, PDB code: 8orl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8orl

Go back to Zinc Binding Sites List in 8orl
Zinc binding site 1 out of 5 in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56


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 the S23226G Missense Variant of Titin Domain FN3- 56 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:13.9
occ:0.99
 OE1 A:GLU83 1.9 15.8 1.0
OD1 C:ASP62 2.0 13.9 1.0
NE2 A:HIS41 2.1 13.5 1.0
CL C:CL202 2.2 18.6 1.0
CG C:ASP62 2.8 14.5 1.0
CD A:GLU83 2.8 15.1 1.0
OD2 C:ASP62 2.9 15.4 1.0
CE1 A:HIS41 3.0 15.8 1.0
OE2 A:GLU83 3.1 15.3 1.0
CD2 A:HIS41 3.1 12.3 1.0
HE1 A:HIS41 3.1 19.0 1.0
HD2 A:HIS41 3.4 14.8 1.0
HG2 A:PRO59 3.4 12.5 1.0
H C:LEU63 3.6 16.1 1.0
HD12 A:ILE88 3.8 21.7 1.0
HG3 A:PRO59 3.8 12.5 1.0
HB3 A:GLU83 4.0 18.0 1.0
HG2 C:ARG64 4.0 22.0 1.0
CG A:PRO59 4.1 10.4 1.0
HB A:ILE88 4.1 19.1 1.0
CG A:GLU83 4.1 16.0 1.0
ND1 A:HIS41 4.1 14.3 1.0
CB C:ASP62 4.2 13.4 1.0
CG A:HIS41 4.2 11.7 1.0
O C:HOH413 4.3 30.8 1.0
HD3 C:ARG64 4.3 21.9 1.0
HA C:ASP62 4.4 14.8 1.0
N C:LEU63 4.4 13.4 1.0
HG2 A:GLU83 4.4 19.1 1.0
HB2 C:LEU63 4.4 14.5 1.0
HB3 C:ASP62 4.5 16.1 1.0
CB A:GLU83 4.5 15.0 1.0
O C:HOH400 4.6 29.8 1.0
HB2 A:GLU83 4.6 18.0 1.0
O A:HOH301 4.7 34.3 1.0
CD1 A:ILE88 4.7 18.1 1.0
CA C:ASP62 4.8 12.3 1.0
HD2 C:ARG64 4.8 21.9 1.0
HB2 C:ASP62 4.8 16.1 1.0
HG3 A:GLU83 4.8 19.1 1.0
CG C:ARG64 4.9 18.4 1.0
CD C:ARG64 4.9 18.3 1.0
HG C:LEU63 4.9 15.3 1.0
HD1 A:HIS41 4.9 17.1 1.0
HG13 A:ILE88 4.9 20.3 1.0
CB A:ILE88 5.0 15.9 1.0
HB3 A:PRO59 5.0 11.7 1.0

Zinc binding site 2 out of 5 in 8orl

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Zinc binding site 2 out of 5 in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56


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 the S23226G Missense Variant of Titin Domain FN3- 56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:29.5
occ:0.33
 HE1 B:HIS41 1.8 26.6 1.0
HE2 B:HIS41 2.0 29.8 1.0
OE1 B:GLU83 2.0 23.1 1.0
CE1 B:HIS41 2.2 22.1 1.0
HD11 B:ILE88 2.3 28.0 1.0
NE2 B:HIS41 2.3 24.8 1.0
CD B:GLU83 3.0 22.8 1.0
CD1 B:ILE88 3.1 23.3 1.0
HD13 B:ILE88 3.2 28.0 1.0
HG3 B:PRO59 3.2 30.9 1.0
HG12 B:ILE88 3.3 25.1 1.0
OE2 B:GLU83 3.5 26.0 1.0
ND1 B:HIS41 3.5 21.8 1.0
CG1 B:ILE88 3.6 20.9 1.0
CD2 B:HIS41 3.6 21.5 1.0
HG13 B:ILE88 3.7 25.1 1.0
HD12 B:ILE88 3.8 28.0 1.0
HB2 B:GLU83 4.0 16.5 1.0
CG B:PRO59 4.2 25.8 1.0
CG B:GLU83 4.2 17.4 1.0
CG B:HIS41 4.2 18.3 1.0
HD2 B:HIS41 4.2 25.8 1.0
HG2 B:PRO59 4.4 30.9 1.0
HB3 B:PRO59 4.4 28.3 1.0
HG3 B:GLU83 4.5 20.9 1.0
O B:HOH399 4.5 37.5 1.0
CB B:GLU83 4.5 13.7 1.0
HB3 B:GLU83 4.7 16.5 1.0
O B:HOH423 4.8 22.3 1.0
CB B:PRO59 4.8 23.6 1.0
HD3 B:PRO59 5.0 31.4 1.0
HG2 B:GLU83 5.0 20.9 1.0

Zinc binding site 3 out of 5 in 8orl

Go back to Zinc Binding Sites List in 8orl
Zinc binding site 3 out of 5 in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56


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 the S23226G Missense Variant of Titin Domain FN3- 56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:19.7
occ:0.79
 OD2 C:ASP32 1.8 18.0 1.0
OE1 B:GLU36 1.9 22.5 1.0
CL C:CL204 2.1 40.1 0.7
CL C:CL203 2.1 33.6 0.8
CG C:ASP32 2.8 17.1 1.0
CD B:GLU36 2.8 21.1 1.0
HH22 C:ARG28 3.1 28.2 1.0
OD1 C:ASP32 3.1 17.3 1.0
OE2 B:GLU36 3.2 21.5 1.0
HH12 C:ARG28 3.6 24.6 1.0
O C:HOH409 3.8 31.1 1.0
NH2 C:ARG28 3.9 23.5 1.0
HD2 B:ARG85 4.0 32.3 1.0
O B:HOH395 4.1 26.8 1.0
CB C:ASP32 4.2 15.9 1.0
CG B:GLU36 4.2 18.0 1.0
NH1 C:ARG28 4.3 20.5 1.0
HB3 B:GLU36 4.3 19.0 1.0
HB3 C:ASP32 4.4 19.1 1.0
O B:HOH433 4.4 26.4 1.0
HG2 B:GLU36 4.4 21.6 1.0
HB2 C:ASP32 4.4 19.1 1.0
HH21 C:ARG28 4.4 28.2 1.0
O C:HOH406 4.5 41.8 1.0
O C:SER35 4.5 15.0 1.0
CZ C:ARG28 4.6 21.2 1.0
HA2 C:GLY34 4.6 20.0 1.0
O A:HOH444 4.6 36.6 1.0
O C:HOH362 4.6 15.7 1.0
H C:GLY34 4.7 19.6 1.0
HD3 B:ARG85 4.7 32.3 1.0
HA C:GLU36 4.8 13.0 1.0
CB B:GLU36 4.8 15.8 1.0
CD B:ARG85 4.8 26.9 1.0
C C:SER35 4.8 13.6 1.0
HG3 B:GLU36 4.9 21.6 1.0
N C:SER35 4.9 15.6 1.0
H C:SER35 4.9 18.7 1.0
HH11 C:ARG28 5.0 24.6 1.0

Zinc binding site 4 out of 5 in 8orl

Go back to Zinc Binding Sites List in 8orl
Zinc binding site 4 out of 5 in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56


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 the S23226G Missense Variant of Titin Domain FN3- 56 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:22.8
occ:0.70
 ND1 B:HIS41 2.2 21.8 1.0
CL B:CL204 2.2 24.1 0.8
O B:HOH423 2.4 22.3 1.0
O B:HOH440 2.6 27.8 1.0
HB3 B:HIS41 2.7 16.2 1.0
CG B:HIS41 3.1 18.3 1.0
CE1 B:HIS41 3.2 22.1 1.0
CB B:HIS41 3.3 13.5 1.0
HE1 B:HIS41 3.4 26.6 1.0
HD2 B:ARG54 3.5 37.1 1.0
O B:HOH373 3.7 50.2 1.0
HA B:HIS41 3.7 13.2 1.0
HD3 B:ARG54 3.7 37.1 1.0
HD3 B:PRO59 3.9 31.4 1.0
HG2 B:ARG54 3.9 35.7 1.0
CD B:ARG54 4.0 31.0 1.0
HB2 B:HIS41 4.1 16.2 1.0
CA B:HIS41 4.1 11.0 1.0
CD2 B:HIS41 4.2 21.5 1.0
NE2 B:HIS41 4.2 24.8 1.0
HG3 B:PRO59 4.4 30.9 1.0
HB3 B:PRO59 4.5 28.3 1.0
CG B:ARG54 4.5 29.8 1.0
H B:VAL42 4.6 13.8 1.0
HD13 B:ILE88 4.6 28.0 1.0
CD B:PRO59 4.7 26.2 1.0
O B:HOH432 4.7 44.5 1.0
HA B:PRO59 4.9 27.2 1.0
CG B:PRO59 4.9 25.8 1.0
C B:HIS41 5.0 10.8 1.0

Zinc binding site 5 out of 5 in 8orl

Go back to Zinc Binding Sites List in 8orl
Zinc binding site 5 out of 5 in the Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the S23226G Missense Variant of Titin Domain FN3- 56 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:12.9
occ:0.99
 OE2 C:GLU83 1.8 12.1 0.6
NE2 C:HIS41 2.1 11.4 1.0
OE1 C:GLU83 2.3 15.1 0.4
CD C:GLU83 2.6 11.6 0.6
OE2 C:GLU83 2.7 13.9 0.4
OE1 C:GLU83 2.8 12.0 0.6
CD C:GLU83 2.8 14.4 0.4
CE1 C:HIS41 3.1 11.4 1.0
CD2 C:HIS41 3.1 11.3 1.0
HG3 C:PRO59 3.1 21.7 1.0
HD2 C:HIS41 3.2 13.6 1.0
HE1 C:HIS41 3.2 13.6 1.0
O C:HOH355 4.0 17.1 1.0
CG C:GLU83 4.0 11.0 0.6
CG C:PRO59 4.1 18.1 1.0
HD12 C:ILE88 4.1 17.6 1.0
ND1 C:HIS41 4.2 11.7 1.0
CG C:HIS41 4.2 9.8 1.0
HG2 C:GLU83 4.2 13.2 0.6
HG3 C:GLU83 4.3 13.2 0.6
HB3 C:PRO59 4.3 19.7 1.0
CG C:GLU83 4.3 13.7 0.4
HG2 C:PRO59 4.4 21.7 1.0
HH12 C:ARG54 4.5 15.4 1.0
O C:HOH408 4.5 27.4 1.0
HD3 C:PRO59 4.6 20.1 1.0
HG2 C:GLU83 4.6 16.5 0.4
HB C:ILE88 4.7 15.9 1.0
HB3 C:GLU83 4.7 15.1 0.4
CB C:PRO59 4.8 16.4 1.0
HG3 C:GLU83 4.8 16.5 0.4
CD C:PRO59 4.9 16.8 1.0
HD1 C:HIS41 5.0 14.1 1.0

Reference:

M.Rees, R.Nikoopour, A.Alexandrovich, M.Pfuhl, L.R.Lopes, M.M.Akhtar, P.Syrris, P.Elliott, G.Carr-White, M.Gautel. Structure Determination and Analysis of Titin A-Band Fibronectin Type III Domains Provides Insights For Disease-Linked Variants and Protein Oligomerisation. J.Struct.Biol. 08009 2023.
ISSN: ESSN 1095-8657
PubMed: 37549721
DOI: 10.1016/J.JSB.2023.108009
Page generated: Thu Dec 28 13:30:00 2023

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