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Chlorine in PDB 6ylm: Mcherry

Protein crystallography data

The structure of Mcherry, PDB code: 6ylm was solved by J.Myskova, M.Rybakova, J.Brynda, J.Lazar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.12 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.280, 42.920, 85.770, 90.00, 128.50, 90.00
R / Rfree (%) 20.1 / 21.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Mcherry (pdb code 6ylm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Mcherry, PDB code: 6ylm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6ylm

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Chlorine binding site 1 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:34.5
occ:1.00
 O A:HOH533 2.8 41.1 1.0
N A:GLY191 3.1 20.9 1.0
O A:HOH477 3.3 31.4 1.0
CD A:PRO80 3.7 31.7 1.0
CA A:GLY191 3.9 19.8 1.0
CB A:PRO190 3.9 22.4 1.0
CG1 A:ILE79 4.0 32.1 1.0
CA A:ILE79 4.0 31.6 1.0
CA A:PRO190 4.0 21.5 1.0
C A:PRO190 4.1 21.8 1.0
CG2 A:ILE79 4.1 33.5 1.0
CB A:ILE79 4.2 31.6 1.0
C A:GLY191 4.3 19.1 1.0
O A:ASP78 4.3 31.0 1.0
O A:GLY191 4.5 20.3 1.0
N A:PRO80 4.6 31.8 1.0
CD1 A:ILE79 4.8 30.9 1.0
C A:ILE79 4.8 30.5 1.0
CG A:PRO80 4.9 34.2 1.0
CD1 A:TYR193 4.9 22.0 1.0
N A:ILE79 5.0 29.8 1.0

Chlorine binding site 2 out of 8 in 6ylm

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Chlorine binding site 2 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:34.9
occ:1.00
 O A:HOH538 2.8 35.7 1.0
O A:HOH446 3.0 23.1 1.0
N A:ILE201 3.2 26.1 1.0
CA A:GLY142 3.8 23.5 1.0
CA A:ASP200 3.9 26.1 1.0
CB A:ILE201 3.9 28.6 1.0
CG1 A:ILE201 3.9 28.4 1.0
C A:ASP200 4.0 26.8 1.0
CA A:ILE201 4.0 26.4 1.0
O A:HOH450 4.1 33.3 1.0
O A:ILE201 4.2 27.1 1.0
O A:LEU199 4.4 22.4 1.0
C A:ILE201 4.6 26.3 1.0
CB A:ASP200 4.6 27.4 1.0
O A:MET141 4.7 29.2 1.0
N A:GLY142 4.7 24.2 1.0
O A:HOH416 4.7 24.1 1.0
O A:HOH417 4.7 34.9 1.0
C A:GLY142 4.7 22.3 1.0
OD1 A:ASP200 4.8 30.4 1.0
N A:TRP143 4.8 22.0 1.0
N A:ASP200 4.9 24.4 1.0
C A:MET141 5.0 27.1 1.0

Chlorine binding site 3 out of 8 in 6ylm

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Chlorine binding site 3 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:25.9
occ:1.00
 N A:ASN128 3.3 21.0 1.0
CB A:THR127 3.7 21.6 1.0
CA A:THR127 3.7 20.7 1.0
CA A:ASN23 3.9 24.1 1.0
O A:HOH460 3.9 37.9 1.0
OD1 A:ASN23 3.9 23.5 1.0
C A:THR127 4.0 20.5 1.0
CG2 A:THR127 4.1 22.4 1.0
CA A:ASN128 4.2 21.8 1.0
CG A:ASN23 4.3 25.5 1.0
C A:ASN23 4.4 26.2 1.0
CB A:ASN23 4.6 24.6 1.0
N A:ASN23 4.7 22.9 1.0
N A:GLY24 4.8 24.5 1.0
O A:GLY126 4.9 19.6 1.0

Chlorine binding site 4 out of 8 in 6ylm

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Chlorine binding site 4 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:32.5
occ:1.00
 O A:HOH492 2.6 40.0 1.0
OH A:TYR193 2.8 24.9 1.0
NE2 A:HIS75 3.0 27.2 1.0
O A:HOH531 3.2 26.0 0.5
O A:HOH511 3.4 23.9 1.0
CE1 A:HIS75 3.7 27.0 1.0
CZ A:TYR193 3.8 22.7 1.0
CE2 A:TYR193 3.9 21.6 1.0
CG2 A:VAL195 4.0 20.2 1.0
O A:HOH456 4.1 26.0 1.0
CG1 A:VAL73 4.1 24.2 1.0
CD2 A:HIS75 4.2 27.1 1.0
CE A:MET150 4.5 23.5 1.0
CB A:VAL73 4.5 23.2 1.0
CD2 A:LEU157 4.6 23.4 1.0
CG2 A:VAL73 4.6 24.8 1.0
CG A:MET150 4.7 22.1 1.0
CD1 A:LEU83 4.8 23.6 1.0
SD A:MET150 4.9 26.6 1.0
ND1 A:HIS75 4.9 28.4 1.0

Chlorine binding site 5 out of 8 in 6ylm

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Chlorine binding site 5 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:43.7
occ:0.50
 NH1 A:ARG13 2.2 41.4 0.5
CD A:ARG13 2.7 34.2 0.5
O A:HOH469 3.0 37.4 1.0
CZ A:ARG13 3.1 39.3 0.5
CG A:ARG13 3.2 33.1 0.5
O A:HOH405 3.3 33.9 1.0
NE A:ARG13 3.3 37.2 0.5
O A:HOH458 3.8 36.8 1.0
CD A:ARG13 4.2 27.5 0.5
NH2 A:ARG13 4.3 40.8 0.5
NE A:ARG13 4.5 28.2 0.5
CG A:ARG13 4.5 26.5 0.5
O A:HOH499 4.6 34.7 0.5
CB A:ARG13 4.6 30.5 0.5
CE2 A:PHE11 4.7 29.9 1.0
CD2 A:PHE11 4.7 30.3 1.0
O A:GLY116 4.7 33.4 1.0
CB A:ARG13 4.8 26.7 0.5
N A:ARG13 4.9 27.9 0.5
N A:ARG13 4.9 26.6 0.5
O A:PHE11 5.0 29.4 1.0

Chlorine binding site 6 out of 8 in 6ylm

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Chlorine binding site 6 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:49.9
occ:1.00
 N A:GLU10 3.3 34.2 1.0
CB A:LYS9 3.6 39.0 1.0
CB A:GLU10 3.9 40.0 1.0
CA A:LYS9 3.9 35.5 1.0
C A:LYS9 4.1 35.2 1.0
CA A:GLU10 4.1 35.8 1.0
CG A:GLU10 4.2 46.0 1.0
CD A:LYS9 4.2 44.7 1.0
CG A:LYS9 4.5 41.9 1.0
CD A:GLU10 4.8 52.5 1.0
N A:PHE11 4.9 31.9 1.0
O A:HOH499 4.9 34.7 0.5
OE2 A:GLU10 4.9 57.0 1.0

Chlorine binding site 7 out of 8 in 6ylm

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Chlorine binding site 7 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:38.9
occ:1.00
 O A:HOH425 3.1 38.9 1.0
N A:HIS221 3.2 22.5 1.0
N A:TYR230 3.4 38.0 1.0
ND1 A:HIS221 3.7 29.1 1.0
O A:GLU228 3.7 37.9 1.0
CA A:ARG220 3.7 23.4 1.0
CD A:ARG220 3.8 37.9 1.0
C A:ARG220 3.9 22.2 1.0
CB A:ARG220 4.0 26.1 1.0
CA A:TYR230 4.1 38.7 1.0
CB A:HIS221 4.1 24.7 1.0
CA A:HIS221 4.2 23.1 1.0
C A:LEU229 4.2 37.5 1.0
CA A:LEU229 4.2 37.2 1.0
N A:LYS231 4.3 39.5 1.0
CG A:HIS221 4.3 25.9 1.0
NH1 A:ARG220 4.5 53.9 1.0
CG A:ARG220 4.5 31.4 1.0
O A:HIS221 4.5 22.6 1.0
CD1 A:LEU229 4.6 38.1 1.0
CG A:PRO76 4.6 30.0 1.0
C A:GLU228 4.6 37.2 1.0
C A:TYR230 4.7 42.4 1.0
CE1 A:HIS221 4.8 27.9 1.0
C A:HIS221 4.9 21.8 1.0
NE A:ARG220 4.9 45.7 1.0
N A:LEU229 4.9 36.9 1.0
O A:GLY219 5.0 26.2 1.0

Chlorine binding site 8 out of 8 in 6ylm

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Chlorine binding site 8 out of 8 in the Mcherry


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Mcherry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:36.2
occ:1.00
 O A:HOH502 3.1 38.7 1.0
ND2 A:ASN23 3.1 25.4 1.0
CB A:SER131 3.8 33.1 1.0
CA A:SER131 3.8 31.8 1.0
CE A:MET136 4.0 28.8 1.0
CB A:ASN23 4.1 24.6 1.0
CG A:ASN23 4.1 25.5 1.0
CG A:MET136 4.2 26.7 1.0
N A:SER131 4.6 29.0 1.0
SD A:MET136 4.6 26.4 1.0
CB A:MET136 4.7 26.4 1.0
O A:PHE129 4.7 22.9 1.0
O A:SER131 4.8 31.2 1.0
C A:SER131 4.9 30.1 1.0

Reference:

J.Myskova, O.Rybakova, J.Brynda, P.Khoroshyy, A.Bondar, J.Lazar. Directionality of Light Absorption and Emission in Representative Fluorescent Proteins. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 33273123
DOI: 10.1073/PNAS.2017379117
Page generated: Mon Jul 29 17:48:05 2024

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