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Chlorine in PDB 4e0t: Crystal Structure of Cdpnpt in Its Unbound State

Protein crystallography data

The structure of Crystal Structure of Cdpnpt in Its Unbound State, PDB code: 4e0t was solved by J.M.Schuller, G.Zocher, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.510, 137.020, 172.630, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.3

Other elements in 4e0t:

The structure of Crystal Structure of Cdpnpt in Its Unbound State also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Cdpnpt in Its Unbound State (pdb code 4e0t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Cdpnpt in Its Unbound State, PDB code: 4e0t:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 1 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:67.8
occ:1.00
 NZ A:LYS364 3.0 47.1 1.0
OG A:SER433 3.0 47.3 1.0
OH A:TYR435 3.0 59.7 1.0
OG A:SER421 3.4 39.5 1.0
O A:HOH935 3.4 39.5 1.0
CE2 A:TYR431 3.5 47.5 1.0
CB A:SER433 3.6 36.6 1.0
CE A:LYS364 3.6 40.2 1.0
ND2 A:ASN120 3.8 43.1 1.0
CD A:LYS364 3.9 34.1 1.0
O A:HOH918 3.9 39.1 1.0
O A:HOH913 4.1 73.6 1.0
CZ A:TYR435 4.2 48.7 1.0
OH A:TYR431 4.3 57.0 1.0
CD2 A:TYR431 4.4 47.1 1.0
CZ A:TYR431 4.4 58.0 1.0
OH A:TYR366 4.5 38.5 1.0
CB A:SER421 4.6 34.3 1.0
CE1 A:TYR435 4.8 41.8 1.0
CG A:ASN120 4.9 59.5 1.0

Chlorine binding site 2 out of 12 in 4e0t

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Chlorine binding site 2 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:71.7
occ:1.00
 O A:HOH778 3.2 44.9 1.0
N A:ALA281 3.3 58.8 1.0
CB A:ASP279 3.3 57.1 1.0
NH2 C:ARG185 3.5 77.0 1.0
OD2 A:ASP279 3.5 95.0 1.0
CB A:ALA281 3.5 63.4 1.0
N A:PRO280 3.6 48.3 1.0
CD A:PRO280 3.6 49.3 1.0
C A:ASP279 3.7 52.2 1.0
CG A:ASP279 3.9 82.6 1.0
CA A:ASP279 3.9 51.2 1.0
CB C:LYS182 4.0 59.4 1.0
CA A:ALA281 4.0 61.5 1.0
NH1 C:ARG185 4.2 80.9 1.0
C A:PRO280 4.2 57.7 1.0
CA A:PRO280 4.3 48.7 1.0
CZ C:ARG185 4.3 98.1 1.0
O A:ASP279 4.4 51.0 1.0
N C:LYS182 4.5 55.9 1.0
CB A:PRO280 4.5 50.1 1.0
CG C:LYS182 4.5 74.9 1.0
CG A:PRO280 4.5 53.7 1.0
CA C:LYS182 4.6 57.0 1.0
CB C:ALA181 4.9 55.4 1.0
CD C:LYS182 4.9 86.8 1.0

Chlorine binding site 3 out of 12 in 4e0t

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Chlorine binding site 3 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:55.8
occ:1.00
 NE2 A:GLN159 3.0 29.8 1.0
N A:ILE167 3.0 29.4 1.0
O A:HOH901 3.1 50.8 1.0
O A:HOH792 3.3 57.8 1.0
O A:HOH823 3.5 46.3 1.0
OD1 A:ASN166 3.7 36.1 1.0
CG1 A:ILE167 3.7 27.8 1.0
CA A:ASN166 3.7 30.0 1.0
C A:ASN166 3.8 31.8 1.0
CG A:ASN166 3.9 39.8 1.0
CA A:ILE167 4.0 27.3 1.0
CD A:GLN159 4.1 39.7 1.0
N A:GLU168 4.1 29.6 1.0
OE1 A:GLN159 4.3 31.2 1.0
C A:ILE167 4.3 31.4 1.0
CB A:ASN166 4.3 31.0 1.0
CB A:ILE167 4.4 28.1 1.0
O A:HOH707 4.4 34.3 1.0
O A:VAL165 4.4 35.0 1.0
CG A:GLU168 4.5 35.8 1.0
ND2 A:ASN166 4.6 39.7 1.0
N A:ASN166 4.9 30.7 1.0
OE2 A:GLU168 4.9 41.5 1.0
CD1 A:ILE167 5.0 24.4 1.0
CG2 A:ILE167 5.0 25.7 1.0

Chlorine binding site 4 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 4 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl505

b:71.7
occ:1.00
 OG B:SER433 3.0 51.4 1.0
NZ B:LYS364 3.1 53.0 1.0
OH B:TYR435 3.1 60.2 1.0
ND2 B:ASN120 3.4 72.3 0.5
O B:HOH764 3.5 54.3 1.0
OG B:SER421 3.5 56.0 1.0
CE2 B:TYR431 3.6 69.6 1.0
CB B:SER433 3.6 48.4 1.0
CE B:LYS364 3.7 49.9 1.0
O B:HOH740 3.9 51.1 1.0
CD B:LYS364 4.0 47.0 1.0
CZ B:TYR435 4.3 56.1 1.0
OH B:TYR431 4.4 78.4 1.0
CD2 B:TYR431 4.4 70.9 1.0
CZ B:TYR431 4.5 77.3 1.0
CB B:SER421 4.6 48.0 1.0
CG B:ASN120 4.7 79.2 0.5
OH B:TYR366 4.8 58.2 1.0
CE1 B:TYR435 5.0 50.3 1.0
CA B:SER433 5.0 48.5 1.0

Chlorine binding site 5 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 5 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:80.6
occ:1.00
 O B:HOH676 3.0 41.3 1.0
N B:ALA281 3.4 62.3 1.0
NH2 D:ARG185 3.4 88.3 1.0
CB B:ASP279 3.5 56.6 1.0
CD B:PRO280 3.5 52.7 1.0
N B:PRO280 3.6 52.4 1.0
CB B:ALA281 3.6 66.7 1.0
OD1 B:ASP279 3.7 82.0 1.0
C B:ASP279 3.8 55.1 1.0
CB D:LYS182 3.9 53.3 1.0
NH1 D:ARG185 4.0 88.6 1.0
CA B:ASP279 4.1 51.5 1.0
CG B:ASP279 4.1 78.6 1.0
CA B:ALA281 4.1 65.3 1.0
CZ D:ARG185 4.2 0.3 1.0
N D:LYS182 4.2 47.1 1.0
CA B:PRO280 4.3 53.3 1.0
C B:PRO280 4.3 62.7 1.0
CA D:LYS182 4.4 50.2 1.0
CG D:LYS182 4.4 70.1 1.0
CB B:PRO280 4.4 54.5 1.0
CG B:PRO280 4.4 57.3 1.0
O B:ASP279 4.6 55.4 1.0
CB D:ALA181 4.8 47.5 1.0
OE1 B:GLU168 4.9 57.7 1.0
CD D:LYS182 5.0 82.8 1.0

Chlorine binding site 6 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 6 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl507

b:56.5
occ:1.00
 O B:HOH741 2.8 48.4 1.0
O B:HOH713 3.1 60.6 1.0
N B:ILE167 3.1 30.5 1.0
NE2 B:GLN159 3.1 27.0 1.0
O B:HOH711 3.4 40.8 1.0
OD1 B:ASN166 3.5 38.2 1.0
CG1 B:ILE167 3.7 28.8 1.0
CA B:ASN166 3.8 32.4 1.0
CG B:ASN166 3.9 46.9 1.0
C B:ASN166 3.9 35.7 1.0
N B:GLU168 4.0 32.3 1.0
CA B:ILE167 4.0 28.7 1.0
CD B:GLN159 4.1 38.8 1.0
C B:ILE167 4.3 32.9 1.0
O B:HOH679 4.3 40.1 1.0
CB B:ASN166 4.4 33.5 1.0
OE1 B:GLN159 4.4 30.4 1.0
CG B:GLU168 4.4 46.5 1.0
CB B:ILE167 4.4 29.9 1.0
ND2 B:ASN166 4.5 38.0 1.0
O B:VAL165 4.5 39.7 1.0
OE2 B:GLU168 4.8 46.3 1.0
N B:ASN166 4.9 32.6 1.0
CA B:GLU168 5.0 34.5 1.0

Chlorine binding site 7 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 7 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl701

b:64.1
occ:1.00
 O C:HOH852 3.1 33.2 1.0
N C:ALA281 3.3 54.9 1.0
NH2 A:ARG185 3.3 54.9 1.0
CB C:ASP279 3.4 49.6 1.0
CB C:ALA281 3.5 58.0 1.0
N C:PRO280 3.6 45.4 1.0
CD C:PRO280 3.6 46.6 1.0
OD1 C:ASP279 3.6 73.9 1.0
C C:ASP279 3.7 47.1 1.0
NH1 A:ARG185 3.8 50.8 1.0
CA C:ASP279 4.0 44.7 1.0
CG C:ASP279 4.0 71.9 1.0
CB A:LYS182 4.0 45.7 1.0
CA C:ALA281 4.0 57.2 1.0
CZ A:ARG185 4.0 66.8 1.0
C C:PRO280 4.2 55.9 1.0
CA C:PRO280 4.2 47.1 1.0
N A:LYS182 4.3 39.7 1.0
CB C:PRO280 4.4 48.2 1.0
CA A:LYS182 4.4 42.5 1.0
O C:ASP279 4.4 45.2 1.0
CG C:PRO280 4.5 51.2 1.0
CG A:LYS182 4.6 59.6 1.0
CB A:ALA181 4.6 37.4 1.0
C A:ALA181 5.0 42.6 1.0

Chlorine binding site 8 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 8 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl706

b:72.7
occ:1.00
 NZ C:LYS364 3.0 65.2 1.0
OH C:TYR435 3.1 61.1 1.0
OG C:SER433 3.1 53.7 1.0
OG C:SER421 3.4 50.1 1.0
CE2 C:TYR431 3.6 66.5 1.0
ND2 C:ASN120 3.7 46.6 0.5
CE C:LYS364 3.7 49.2 1.0
CB C:SER433 3.7 45.7 1.0
CD C:LYS364 3.9 41.8 1.0
O C:HOH950 3.9 73.3 1.0
O C:HOH933 4.0 51.8 1.0
CZ C:TYR435 4.3 55.8 1.0
CD2 C:TYR431 4.4 66.3 1.0
OH C:TYR431 4.5 77.2 1.0
CZ C:TYR431 4.5 78.0 1.0
CB C:SER421 4.6 39.6 1.0
OH C:TYR366 4.7 54.9 1.0
CG C:ASN120 4.9 56.2 0.5
CE1 C:TYR435 4.9 52.2 1.0

Chlorine binding site 9 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 9 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl707

b:51.8
occ:1.00
 N C:ILE167 3.0 27.8 1.0
NE2 C:GLN159 3.1 26.5 1.0
O C:HOH923 3.1 47.3 1.0
O C:HOH897 3.3 39.8 1.0
O C:HOH904 3.4 36.7 1.0
OD1 C:ASN166 3.5 39.2 1.0
CA C:ASN166 3.7 29.2 1.0
CG1 C:ILE167 3.7 24.8 1.0
C C:ASN166 3.8 31.9 1.0
CG C:ASN166 3.8 38.5 1.0
CA C:ILE167 3.9 26.4 1.0
N C:GLU168 4.0 27.0 1.0
CD C:GLN159 4.2 32.9 1.0
C C:ILE167 4.2 29.9 1.0
CB C:ASN166 4.3 28.1 1.0
CB C:ILE167 4.4 26.7 1.0
O C:HOH905 4.4 51.9 1.0
O C:HOH903 4.4 34.8 1.0
OE1 C:GLN159 4.4 28.8 1.0
CG C:GLU168 4.4 32.2 1.0
O C:VAL165 4.5 34.5 1.0
ND2 C:ASN166 4.5 37.4 1.0
N C:ASN166 4.8 29.4 1.0
OE2 C:GLU168 4.9 32.7 1.0
CA C:GLU168 4.9 28.5 1.0
O C:ASN166 5.0 32.6 1.0
CG2 C:ILE167 5.0 25.9 1.0
O C:HOH823 5.0 52.6 1.0

Chlorine binding site 10 out of 12 in 4e0t

Go back to Chlorine Binding Sites List in 4e0t
Chlorine binding site 10 out of 12 in the Crystal Structure of Cdpnpt in Its Unbound State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Cdpnpt in Its Unbound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl503

b:51.6
occ:1.00
 O D:HOH810 3.0 45.9 1.0
N D:ILE167 3.1 26.4 1.0
NE2 D:GLN159 3.2 23.2 1.0
O D:HOH770 3.6 39.9 1.0
CG1 D:ILE167 3.6 25.5 1.0
OD1 D:ASN166 3.6 32.9 1.0
O D:HOH728 3.7 45.0 1.0
CA D:ASN166 3.8 28.1 1.0
C D:ASN166 3.9 30.2 1.0
N D:GLU168 4.0 27.8 1.0
CA D:ILE167 4.0 25.0 1.0
CG D:ASN166 4.0 42.9 1.0
CD D:GLN159 4.2 35.8 1.0
C D:ILE167 4.2 29.0 1.0
O D:HOH743 4.3 40.9 1.0
CB D:ILE167 4.3 26.3 1.0
OE1 D:GLN159 4.3 33.7 1.0
CG D:GLU168 4.4 35.5 1.0
O D:HOH797 4.4 50.8 1.0
CB D:ASN166 4.5 25.6 1.0
O D:VAL165 4.6 31.4 1.0
ND2 D:ASN166 4.6 38.2 1.0
OE2 D:GLU168 4.9 38.7 1.0
CD1 D:ILE167 4.9 30.2 1.0
CA D:GLU168 4.9 29.3 1.0
CG2 D:ILE167 5.0 22.3 1.0

Reference:

J.M.Schuller, G.Zocher, M.Liebhold, X.Xie, M.Stahl, S.M.Li, T.Stehle. Structure and Catalytic Mechanism of A Cyclic Dipeptide Prenyltransferase with Broad Substrate Promiscuity. J.Mol.Biol. V. 422 87 2012.
ISSN: ISSN 0022-2836
PubMed: 22683356
DOI: 10.1016/J.JMB.2012.05.033
Page generated: Sun Jul 21 12:26:35 2024

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