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Chlorine in PDB 3a7k: Crystal Structure of Halorhodopsin From Natronomonas Pharaonis

Protein crystallography data

The structure of Crystal Structure of Halorhodopsin From Natronomonas Pharaonis, PDB code: 3a7k was solved by T.Kouyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.830, 99.770, 99.270, 90.00, 127.67, 90.00
R / Rfree (%) 24.9 / 27.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis (pdb code 3a7k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis, PDB code: 3a7k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3a7k

Go back to Chlorine Binding Sites List in 3a7k
Chlorine binding site 1 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:26.5
occ:1.00
 OG1 A:THR126 2.9 28.8 1.0
OG A:SER130 3.1 29.4 1.0
O A:HOH502 3.3 36.4 1.0
NZ A:LYS256 3.5 28.2 1.0
CB A:THR126 3.5 25.4 1.0
CE A:LYS256 3.6 28.1 1.0
O A:THR126 3.7 26.5 1.0
CB A:SER130 3.7 29.3 1.0
C A:THR126 3.7 26.8 1.0
CD1 A:TRP127 3.9 27.1 1.0
CG1 A:VAL77 3.9 28.5 1.0
N A:TRP127 4.0 25.3 1.0
CB A:SER81 4.0 29.0 1.0
OG A:SER81 4.1 26.8 1.0
CA A:SER78 4.2 25.3 1.0
CA A:THR126 4.3 28.0 1.0
CA A:TRP127 4.3 25.2 1.0
O A:HOH504 4.4 25.7 1.0
N A:SER78 4.5 24.1 1.0
O A:VAL77 4.6 28.0 1.0
C15 A:RET292 4.6 25.9 1.0
C A:VAL77 4.6 25.8 1.0
NE1 A:TRP127 4.7 26.1 1.0
CB A:SER78 4.7 25.6 1.0
CB A:VAL77 4.8 27.2 1.0
O A:HOH503 4.8 25.4 1.0
CG2 A:THR126 4.8 28.6 1.0
CD A:LYS256 4.8 26.8 1.0
O A:ARG123 4.8 26.6 1.0
CG A:TRP127 4.9 25.0 1.0
OG A:SER78 4.9 28.2 1.0

Chlorine binding site 2 out of 6 in 3a7k

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Chlorine binding site 2 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:42.0
occ:1.00
 O B:HOH527 2.7 48.2 1.0
O B:HOH531 2.8 63.9 1.0
ND2 A:ASN145 3.1 33.9 1.0
O A:HOH530 3.3 61.3 1.0
CB B:PRO62 3.7 39.3 1.0
CD B:LYS65 3.7 38.9 1.0
CE A:LYS148 3.8 39.5 1.0
CA B:PRO62 3.8 38.7 1.0
CB A:THR147 3.9 32.9 1.0
CG2 A:THR147 4.0 30.2 1.0
CG A:ASN145 4.0 35.8 1.0
CG A:LYS148 4.1 34.3 1.0
C25 B:22B300 4.1 57.7 1.0
OD1 A:ASN145 4.2 32.7 1.0
OG1 A:THR147 4.4 32.8 1.0
NZ B:LYS65 4.5 44.3 1.0
CB B:LYS65 4.6 33.4 1.0
CD A:LYS148 4.6 36.3 1.0
N B:PRO62 4.6 39.0 1.0
CG B:LYS65 4.7 35.6 1.0
CE B:LYS65 4.7 43.2 1.0
CG B:PRO62 4.8 40.5 1.0
O A:HOH529 4.8 55.1 1.0
CD B:PRO62 4.8 39.3 1.0
N A:LYS148 4.9 31.6 1.0
O B:PRO62 4.9 37.6 1.0
C B:PRO62 4.9 38.2 1.0
O27 B:22B300 5.0 60.3 1.0

Chlorine binding site 3 out of 6 in 3a7k

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Chlorine binding site 3 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:28.7
occ:1.00
 O B:HOH502 2.9 28.0 1.0
OG1 B:THR126 3.1 25.3 1.0
OG B:SER130 3.1 27.0 1.0
NZ B:LYS256 3.4 29.5 1.0
CE B:LYS256 3.6 28.2 1.0
CB B:THR126 3.7 28.2 1.0
CB B:SER130 3.7 26.0 1.0
CD1 B:TRP127 3.7 29.7 1.0
O B:THR126 3.9 29.3 1.0
C B:THR126 3.9 28.9 1.0
CB B:SER81 3.9 24.5 1.0
OG B:SER81 4.0 26.5 1.0
CG1 B:VAL77 4.1 27.0 1.0
N B:TRP127 4.2 28.0 1.0
CA B:SER78 4.2 29.0 1.0
NE1 B:TRP127 4.4 30.4 1.0
C15 B:RET292 4.4 25.7 1.0
CA B:TRP127 4.4 27.9 1.0
CA B:THR126 4.5 29.6 1.0
O B:VAL77 4.5 26.7 1.0
N B:SER78 4.5 27.8 1.0
O B:HOH504 4.5 32.8 1.0
C B:VAL77 4.6 29.5 1.0
CB B:SER78 4.7 27.5 1.0
CD B:LYS256 4.8 29.8 1.0
OG B:SER78 4.8 29.0 1.0
CG B:TRP127 4.9 29.7 1.0
O B:ARG123 4.9 33.5 1.0
O B:HOH503 4.9 30.6 1.0
C14 B:RET292 4.9 24.6 1.0
CG2 B:THR126 5.0 26.5 1.0

Chlorine binding site 4 out of 6 in 3a7k

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Chlorine binding site 4 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:62.5
occ:1.00
 ND2 B:ASN145 3.3 42.6 1.0
CB B:THR147 3.7 42.9 1.0
CE B:LYS148 3.7 42.6 1.0
O27 D:22B300 3.7 0.5 1.0
CG2 B:THR147 3.8 43.1 1.0
CA D:PRO62 3.9 53.9 1.0
CB D:PRO62 3.9 53.6 1.0
NZ D:LYS65 3.9 59.9 1.0
CG B:LYS148 3.9 39.6 1.0
OD1 B:ASN145 3.9 43.8 1.0
CG B:ASN145 4.1 42.0 1.0
C25 D:22B300 4.1 0.2 1.0
CG D:LYS65 4.2 52.8 1.0
CB D:LYS65 4.3 48.4 1.0
OG1 B:THR147 4.3 46.7 1.0
CD B:LYS148 4.4 41.5 1.0
C23 D:22B300 4.6 0.6 1.0
N D:PRO62 4.7 54.1 1.0
NZ B:LYS148 4.7 46.9 1.0
N B:LYS148 4.7 39.5 1.0
O D:PRO62 4.7 51.5 1.0
C D:PRO62 4.8 52.7 1.0
CA B:THR147 4.9 41.7 1.0

Chlorine binding site 5 out of 6 in 3a7k

Go back to Chlorine Binding Sites List in 3a7k
Chlorine binding site 5 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:51.3
occ:1.00
 OG1 D:THR126 2.9 40.0 1.0
O D:HOH502 3.0 49.9 1.0
OG D:SER130 3.1 42.1 1.0
NZ D:LYS256 3.4 48.5 1.0
CE D:LYS256 3.6 51.1 1.0
CD1 D:TRP127 3.7 45.1 1.0
CB D:THR126 3.7 38.9 1.0
CB D:SER130 3.8 43.5 1.0
O D:THR126 3.9 35.7 1.0
C D:THR126 3.9 35.9 1.0
OG D:SER81 4.0 38.4 1.0
CB D:SER81 4.0 39.7 1.0
N D:TRP127 4.1 36.9 1.0
O D:HOH504 4.2 58.0 1.0
NE1 D:TRP127 4.3 44.9 1.0
CA D:TRP127 4.4 37.4 1.0
C15 D:RET292 4.4 47.0 1.0
CA D:SER78 4.4 43.5 1.0
CG1 D:VAL77 4.5 42.8 1.0
CA D:THR126 4.5 37.0 1.0
O D:HOH503 4.5 45.2 1.0
O D:VAL77 4.5 42.4 1.0
N D:SER78 4.7 42.5 1.0
C D:VAL77 4.7 41.7 1.0
CG D:TRP127 4.8 44.6 1.0
O D:ARG123 4.8 46.3 1.0
CB D:SER78 4.8 42.3 1.0
OG D:SER78 4.9 43.9 1.0
C14 D:RET292 4.9 44.9 1.0
CD D:LYS256 4.9 52.6 1.0
CG2 D:THR126 4.9 37.2 1.0

Chlorine binding site 6 out of 6 in 3a7k

Go back to Chlorine Binding Sites List in 3a7k
Chlorine binding site 6 out of 6 in the Crystal Structure of Halorhodopsin From Natronomonas Pharaonis


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 Halorhodopsin From Natronomonas Pharaonis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:65.3
occ:1.00
 OD1 D:ASN145 3.2 45.3 1.0
CB A:PRO62 3.6 45.0 1.0
CE A:LYS65 3.6 47.0 1.0
CA A:PRO62 3.6 44.5 1.0
CE D:LYS148 3.7 52.0 1.0
CB D:THR147 3.8 40.6 1.0
CG2 D:THR147 3.9 40.8 1.0
CG D:ASN145 4.0 42.2 1.0
ND2 D:ASN145 4.1 42.0 1.0
CG D:LYS148 4.1 47.8 1.0
NZ A:LYS65 4.2 52.1 1.0
OG1 D:THR147 4.4 41.3 1.0
CD D:LYS148 4.4 51.5 1.0
N A:PRO62 4.4 46.4 1.0
O D:HOH522 4.6 84.4 1.0
NZ D:LYS148 4.7 55.6 1.0
O A:PRO62 4.7 41.3 1.0
C A:PRO62 4.7 42.3 1.0
O27 A:22B300 4.8 83.0 1.0
C25 A:22B300 4.8 81.9 1.0
CB A:LYS65 4.9 38.9 1.0
N D:LYS148 4.9 40.8 1.0
CG A:PRO62 4.9 46.0 1.0
CD A:PRO62 4.9 45.8 1.0
CD A:LYS65 4.9 46.7 1.0
O A:ASP60 5.0 51.0 1.0

Reference:

T.Kouyama, S.Kanada, Y.Takeguchi, A.Narusawa, M.Murakami, K.Ihara. Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin From Natronomonas Pharaonis. J.Mol.Biol. V. 396 564 2010.
ISSN: ISSN 0022-2836
PubMed: 19961859
DOI: 10.1016/J.JMB.2009.11.061
Page generated: Fri Jul 11 03:01:34 2025

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