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Chlorine in PDB 4kgn: Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine

Enzymatic activity of Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine

All present enzymatic activity of Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine:
2.1.1.207;

Protein crystallography data

The structure of Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine, PDB code: 4kgn was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.17 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.600, 149.710, 80.300, 90.00, 90.49, 90.00
R / Rfree (%) 16.9 / 19.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine (pdb code 4kgn). 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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine, PDB code: 4kgn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4kgn

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Chlorine binding site 1 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:21.4
occ:1.00
 O B:HOH315 2.8 29.4 1.0
N A:ASN134 3.3 17.8 1.0
ND2 A:ASN137 3.3 16.7 1.0
ND2 B:ASN24 3.4 18.2 1.0
CA A:LEU133 3.6 18.0 1.0
CA B:LEU21 3.6 21.4 1.0
CD1 B:LEU21 3.7 22.4 1.0
CB B:LEU21 3.8 21.9 1.0
CD2 A:LEU133 3.9 17.2 1.0
CB A:LEU133 3.9 17.6 1.0
N B:LEU21 3.9 21.4 1.0
C A:LEU133 3.9 18.3 1.0
CB A:ASN134 4.1 17.9 1.0
CA A:ASN134 4.3 17.8 1.0
CG A:ASN137 4.3 16.9 1.0
CB A:ASN137 4.3 16.5 1.0
CG B:LEU21 4.4 23.4 1.0
C B:ARG20 4.5 20.9 1.0
CG B:ARG20 4.5 31.4 1.0
CG B:ASN24 4.5 18.4 1.0
CG A:LEU133 4.6 16.9 1.0
O B:ARG20 4.6 19.7 1.0
O B:ASN17 4.8 19.6 1.0
O A:SER132 4.8 18.0 1.0
CB B:ASN24 4.8 18.8 1.0
N A:LEU133 4.9 18.3 1.0
C B:LEU21 5.0 19.7 1.0

Chlorine binding site 2 out of 6 in 4kgn

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Chlorine binding site 2 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:35.7
occ:1.00
 N B:GLU10 3.2 35.5 1.0
N B:GLU104 3.4 41.2 1.0
N B:ILE11 3.4 34.0 1.0
O B:HOH321 3.5 32.1 1.0
ND2 B:ASN14 3.8 32.1 1.0
CB B:GLU104 3.8 44.6 1.0
CD2 B:LEU135 3.9 30.3 1.0
CA B:GLU10 4.0 37.7 1.0
CB B:GLU10 4.0 38.3 1.0
C B:PRO9 4.1 34.0 1.0
CA B:PRO9 4.1 32.6 1.0
CA B:ALA103 4.1 38.5 1.0
CB B:ILE11 4.1 34.2 1.0
C B:GLU10 4.2 37.2 1.0
CA B:GLU104 4.2 44.8 1.0
C B:ALA103 4.2 39.8 1.0
CA B:ILE11 4.3 33.0 1.0
CD1 B:ILE11 4.3 35.9 1.0
CG1 B:ILE11 4.3 36.0 1.0
CB B:ALA103 4.5 39.5 1.0
CB B:PRO9 4.5 30.9 1.0
O B:ILE11 4.6 27.4 1.0
CB B:ASN14 4.6 29.3 1.0
CG B:ASN14 4.7 32.0 1.0
C B:ILE11 4.9 30.6 1.0
O B:HOH322 5.0 40.7 1.0

Chlorine binding site 3 out of 6 in 4kgn

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Chlorine binding site 3 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:19.3
occ:1.00
 O D:HOH205 2.9 28.6 1.0
ND2 C:ASN137 3.1 17.6 1.0
N C:ASN134 3.2 18.7 1.0
ND2 D:ASN24 3.4 21.6 1.0
CA C:LEU133 3.6 18.6 1.0
CD1 D:LEU21 3.6 25.8 1.0
CA D:LEU21 3.7 23.4 1.0
CB D:LEU21 3.8 23.7 1.0
CD2 C:LEU133 3.9 18.2 1.0
CB C:LEU133 3.9 17.7 1.0
CB C:ASN134 3.9 18.7 1.0
C C:LEU133 3.9 18.9 1.0
N D:LEU21 4.0 23.5 1.0
CG C:ASN137 4.1 17.8 1.0
CB C:ASN137 4.1 17.6 1.0
CA C:ASN134 4.2 18.4 1.0
CG D:ARG20 4.3 35.6 1.0
CG D:LEU21 4.3 25.3 1.0
C D:ARG20 4.4 25.2 1.0
CG C:LEU133 4.5 17.9 1.0
CG D:ASN24 4.6 21.7 1.0
O D:ARG20 4.6 24.0 1.0
CD D:ARG20 4.6 41.8 1.0
O D:ASN17 4.8 26.7 1.0
O C:SER132 4.8 21.9 1.0
CB D:ARG20 4.8 30.4 1.0
N C:LEU133 4.9 19.9 1.0
CB D:ASN24 4.9 21.4 1.0
O C:ASN134 5.0 17.5 1.0
NE D:ARG20 5.0 48.9 1.0

Chlorine binding site 4 out of 6 in 4kgn

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Chlorine binding site 4 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl202

b:23.0
occ:1.00
 O F:HOH309 3.1 25.0 1.0
N E:ASN134 3.2 17.6 1.0
ND2 F:ASN24 3.3 22.5 1.0
ND2 E:ASN137 3.4 18.5 1.0
CA E:LEU133 3.6 18.2 1.0
CA F:LEU21 3.6 22.4 1.0
CD2 E:LEU133 3.8 18.7 1.0
CB F:LEU21 3.8 23.4 1.0
CD1 F:LEU21 3.9 24.3 1.0
C E:LEU133 3.9 18.0 1.0
CB E:LEU133 3.9 17.9 1.0
N F:LEU21 4.0 21.8 1.0
CB E:ASN134 4.1 18.6 1.0
CA E:ASN134 4.2 17.9 1.0
CB E:ASN137 4.3 17.9 1.0
CG E:ASN137 4.4 18.4 1.0
C F:ARG20 4.4 21.6 1.0
CG E:LEU133 4.4 18.8 1.0
CG F:ASN24 4.5 22.6 1.0
CG F:LEU21 4.5 24.4 1.0
O F:ARG20 4.6 20.9 1.0
CB F:ASN24 4.7 22.1 1.0
CB F:ARG20 4.8 23.2 1.0
O E:SER132 4.8 21.3 1.0
N E:LEU133 4.8 19.3 1.0
O F:ASN17 4.9 22.3 1.0
C F:LEU21 4.9 22.1 1.0

Chlorine binding site 5 out of 6 in 4kgn

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Chlorine binding site 5 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:40.1
occ:1.00
 O F:HOH303 3.0 36.9 1.0
N F:GLU10 3.3 35.5 1.0
N F:ILE11 3.3 40.8 1.0
N F:GLU104 3.7 40.2 1.0
ND2 F:ASN14 3.7 40.3 1.0
CB F:ILE11 3.9 44.3 1.0
CD2 F:LEU135 4.0 32.5 1.0
CG1 F:ILE11 4.0 46.6 1.0
CA F:GLU10 4.0 38.3 1.0
CB F:GLU104 4.1 44.7 1.0
CD1 F:ILE11 4.1 46.0 1.0
CB F:GLU10 4.1 38.9 1.0
CA F:ILE11 4.2 42.0 1.0
C F:GLU10 4.2 40.7 1.0
C F:PRO9 4.2 33.5 1.0
CA F:PRO9 4.3 31.2 1.0
CA F:ALA103 4.3 35.3 1.0
O F:ILE11 4.3 41.0 1.0
CB F:ASN14 4.4 36.5 1.0
C F:ALA103 4.5 36.8 1.0
CA F:GLU104 4.5 43.6 1.0
CB F:PRO9 4.5 30.6 1.0
CB F:ALA103 4.6 36.9 1.0
CG F:ASN14 4.6 39.4 1.0
C F:ILE11 4.8 40.3 1.0

Chlorine binding site 6 out of 6 in 4kgn

Go back to Chlorine Binding Sites List in 4kgn
Chlorine binding site 6 out of 6 in the Crystal Structure of A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine


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 A Trna (Cytidine(34)-2'-O)-Methyltransferase Bound to S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl202

b:21.4
occ:1.00
 ND2 G:ASN137 3.1 18.0 1.0
O H:HOH214 3.1 26.5 1.0
N G:ASN134 3.3 18.6 1.0
ND2 H:ASN24 3.5 22.8 1.0
CA G:LEU133 3.6 17.6 1.0
CA H:LEU21 3.6 20.4 1.0
CB H:LEU21 3.8 21.3 1.0
CD2 G:LEU133 3.8 17.7 1.0
CD1 H:LEU21 3.9 21.7 1.0
CB G:LEU133 3.9 17.1 1.0
C G:LEU133 3.9 17.8 1.0
N H:LEU21 4.0 21.2 1.0
CB G:ASN134 4.1 18.1 1.0
CG G:ASN137 4.1 17.6 1.0
CB G:ASN137 4.2 17.7 1.0
CA G:ASN134 4.3 18.8 1.0
CG H:ARG20 4.3 28.8 1.0
CG H:LEU21 4.4 22.4 1.0
C H:ARG20 4.5 22.2 1.0
CG G:LEU133 4.5 17.0 1.0
CG H:ASN24 4.6 21.2 1.0
O H:ARG20 4.6 21.6 1.0
O H:ASN17 4.7 23.9 1.0
O G:SER132 4.8 19.3 1.0
CB H:ASN24 4.8 20.6 1.0
N G:LEU133 4.8 18.6 1.0
C H:LEU21 4.9 19.9 1.0
CB H:ARG20 5.0 26.0 1.0

Reference:

T.E.Edwards, J.W.Fairman, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Trmh Family Trna Methyltransferase Bound to S-Adenosyl Homocysteine To Be Published.
Page generated: Sat Dec 12 10:50:26 2020

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