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Sodium in PDB 8sf6: Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation

Protein crystallography data

The structure of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation, PDB code: 8sf6 was solved by A.R.Buller, A.P.Zmich, C.A.Bingman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.93 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 279.09, 133.12, 115.79, 90, 94.87, 90
R / Rfree (%) 15.4 / 17.9

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation (pdb code 8sf6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation, PDB code: 8sf6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 8sf6

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Sodium binding site 1 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:50.3
occ:1.00
 O F:GLU39 2.3 37.1 1.0
O F:HOH745 2.5 45.5 1.0
OD1 A:ASN358 2.6 51.4 1.0
CG A:ASN358 3.5 48.6 1.0
C F:GLU39 3.5 34.5 1.0
O A:ASN358 3.6 40.4 1.0
CG2 F:THR40 3.8 36.4 1.0
O A:HOH809 3.8 32.9 1.0
ND2 A:ASN358 4.0 53.7 1.0
CA A:ASN358 4.3 38.2 1.0
CG F:GLU39 4.3 51.7 1.0
CA F:THR40 4.4 33.2 1.0
C A:ASN358 4.4 38.9 1.0
N F:THR40 4.4 33.8 1.0
CA F:GLU39 4.5 36.3 1.0
CB A:ASN358 4.5 42.9 1.0
O F:HOH674 4.5 30.9 1.0
CB F:THR40 4.6 35.7 1.0
OE2 F:GLU39 4.9 69.3 1.0
CB F:GLU39 5.0 41.5 1.0

Sodium binding site 2 out of 13 in 8sf6

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Sodium binding site 2 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:55.0
occ:1.00
 O F:HOH666 2.2 49.2 1.0
O A:GLU39 2.3 44.4 1.0
O A:HOH815 2.3 44.4 1.0
OD1 F:ASN358 2.5 50.7 1.0
C A:GLU39 3.5 45.1 1.0
CG F:ASN358 3.6 50.2 1.0
O F:ASN358 3.7 47.6 1.0
O F:HOH724 3.9 39.6 1.0
CG2 A:THR40 4.1 45.7 1.0
ND2 F:ASN358 4.1 54.8 1.0
CA A:GLU39 4.3 45.1 1.0
O A:HOH627 4.4 38.8 1.0
N A:THR40 4.4 42.1 1.0
CG A:GLU39 4.4 61.8 1.0
CA A:THR40 4.4 42.9 1.0
CA F:ASN358 4.5 45.4 1.0
C F:ASN358 4.5 47.4 1.0
CB F:ASN358 4.7 47.9 1.0
CB A:THR40 4.8 44.6 1.0
CB A:GLU39 4.8 52.4 1.0

Sodium binding site 3 out of 13 in 8sf6

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Sodium binding site 3 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:47.6
occ:1.00
 O B:HOH660 2.2 46.0 1.0
O H:GLU39 2.3 29.5 1.0
O H:HOH858 2.4 43.7 1.0
OD1 B:ASN358 2.5 39.9 1.0
O B:ASN358 3.4 36.0 1.0
CG B:ASN358 3.5 37.3 1.0
C H:GLU39 3.5 29.2 1.0
O B:HOH827 3.7 31.4 1.0
CG2 H:THR40 3.8 32.2 1.0
ND2 B:ASN358 4.0 40.9 1.0
CA H:THR40 4.2 27.7 1.0
C B:ASN358 4.2 32.3 1.0
CA B:ASN358 4.2 30.7 1.0
N H:THR40 4.3 27.4 1.0
O B:HOH758 4.3 43.7 1.0
O H:HOH726 4.4 29.8 1.0
CA H:GLU39 4.5 30.7 1.0
CB B:ASN358 4.5 34.3 1.0
CB H:THR40 4.5 30.1 1.0
O B:HOH655 4.6 56.7 1.0
O H:HOH614 4.7 39.9 1.0
OE1 H:GLU39 4.9 54.8 1.0
CB H:GLU39 5.0 36.3 1.0

Sodium binding site 4 out of 13 in 8sf6

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Sodium binding site 4 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:56.2
occ:1.00
 O B:GLU39 2.4 32.2 1.0
O B:HOH858 2.4 44.3 1.0
OD1 H:ASN358 2.8 42.0 1.0
O H:ASN358 3.4 36.7 1.0
C B:GLU39 3.5 32.2 1.0
CG H:ASN358 3.8 42.0 1.0
O B:HOH820 3.8 33.1 1.0
CG2 B:THR40 3.8 33.8 1.0
C H:ASN358 4.3 35.2 1.0
CA B:THR40 4.3 31.0 1.0
N B:THR40 4.3 28.8 1.0
ND2 H:ASN358 4.4 45.8 1.0
CA B:GLU39 4.4 33.9 1.0
CA H:ASN358 4.5 34.8 1.0
O B:HOH694 4.5 31.4 1.0
CB B:THR40 4.6 32.1 1.0
O B:HOH846 4.7 43.4 1.0
CB H:ASN358 4.8 38.5 1.0
OE1 B:GLU39 4.8 60.7 1.0
CB B:GLU39 5.0 39.4 1.0

Sodium binding site 5 out of 13 in 8sf6

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Sodium binding site 5 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:41.8
occ:1.00
 O E:GLU39 2.2 30.0 1.0
O E:HOH835 2.2 45.5 1.0
O E:HOH821 2.3 33.8 1.0
O C:HOH647 2.4 41.1 1.0
O E:HOH798 2.4 40.9 1.0
OD1 C:ASN358 2.4 43.5 1.0
NA C:NA504 3.0 45.7 0.8
C E:GLU39 3.3 29.6 1.0
CG C:ASN358 3.5 41.9 1.0
O C:ASN358 3.7 37.5 1.0
O C:HOH777 3.8 32.0 1.0
CG2 E:THR40 3.9 31.7 1.0
ND2 C:ASN358 4.0 43.1 1.0
N E:THR40 4.2 28.9 1.0
CA E:GLU39 4.2 32.4 1.0
CA E:THR40 4.3 29.2 1.0
O E:HOH696 4.3 26.7 1.0
CA C:ASN358 4.4 35.4 1.0
C C:ASN358 4.5 37.0 1.0
O C:HOH707 4.5 42.9 1.0
OE1 E:GLU39 4.5 57.9 1.0
CB C:ASN358 4.6 37.6 1.0
CB E:THR40 4.6 30.4 1.0
CB E:GLU39 4.7 37.8 1.0
O C:HOH859 5.0 49.4 1.0

Sodium binding site 6 out of 13 in 8sf6

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Sodium binding site 6 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:49.5
occ:1.00
 O E:HOH624 2.1 40.7 1.0
O C:GLU39 2.3 33.3 1.0
O C:HOH832 2.3 36.5 1.0
OD1 E:ASN358 2.4 54.3 1.0
C C:GLU39 3.5 34.8 1.0
CG E:ASN358 3.6 51.5 1.0
O E:ASN358 3.6 37.8 1.0
O E:HOH763 3.9 33.2 1.0
CG2 C:THR40 3.9 36.4 1.0
CG C:GLU39 4.1 51.2 1.0
O C:HOH662 4.3 31.3 1.0
CA C:THR40 4.3 34.4 1.0
CA E:ASN358 4.3 39.2 1.0
N C:THR40 4.3 33.6 1.0
CA C:GLU39 4.4 35.4 1.0
C E:ASN358 4.4 37.4 1.0
ND2 E:ASN358 4.4 66.7 1.0
CB E:ASN358 4.6 44.3 1.0
CB C:THR40 4.7 36.4 1.0
CB C:GLU39 4.9 41.8 1.0

Sodium binding site 7 out of 13 in 8sf6

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Sodium binding site 7 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:45.7
occ:0.80
 O C:HOH859 2.2 49.4 1.0
O E:HOH821 2.3 33.8 1.0
O C:HOH707 2.3 42.9 1.0
O C:HOH647 2.4 41.1 1.0
O E:HOH798 2.6 40.9 1.0
NA C:NA502 3.0 41.8 1.0
O C:ASN358 3.8 37.5 1.0
O E:HOH835 4.3 45.5 1.0
O E:HOH696 4.4 26.7 1.0
O C:VAL360 4.5 32.5 1.0
O E:GLU39 4.6 30.0 1.0
OD1 C:ASN358 4.9 43.5 1.0
C C:ASN358 4.9 37.0 1.0

Sodium binding site 8 out of 13 in 8sf6

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Sodium binding site 8 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:51.3
occ:1.00
 O C:HOH825 2.1 43.0 1.0
O C:HOH753 2.2 44.6 1.0
O C:VAL313 2.2 35.8 1.0
O C:HOH769 2.4 41.5 1.0
O C:HIS310 2.4 40.5 1.0
C C:VAL313 3.4 35.3 1.0
C C:HIS310 3.5 40.1 1.0
O C:ASN308 4.1 35.9 1.0
CA C:VAL313 4.2 34.5 1.0
N C:VAL313 4.2 35.4 1.0
CA C:PRO311 4.2 42.7 1.0
CB C:VAL313 4.2 34.1 1.0
N C:HIS310 4.2 39.6 1.0
N C:PRO311 4.3 41.3 1.0
O C:GLU314 4.4 36.3 1.0
N C:GLU314 4.4 33.7 1.0
NZ C:LYS347 4.4 66.7 1.0
CA C:HIS310 4.5 38.7 1.0
O C:LEU307 4.5 32.5 1.0
C C:PRO311 4.5 41.3 1.0
C C:GLU314 4.6 36.6 1.0
C C:ASN308 4.6 35.9 1.0
CA C:GLU314 4.6 37.1 1.0
C C:ASP309 4.7 41.1 1.0
CG1 C:VAL313 4.8 32.6 1.0
O C:PRO311 4.8 40.8 1.0
CE C:LYS347 4.8 62.6 1.0

Sodium binding site 9 out of 13 in 8sf6

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Sodium binding site 9 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:39.4
occ:1.00
 O G:HOH640 2.2 38.8 1.0
O D:GLU39 2.4 31.0 1.0
O G:HOH865 2.4 42.1 1.0
O D:HOH816 2.4 35.2 1.0
OD1 G:ASN358 2.4 39.4 1.0
O D:HOH772 2.4 38.5 1.0
NA G:NA503 3.0 47.9 0.8
CG G:ASN358 3.4 38.3 1.0
C D:GLU39 3.5 30.0 1.0
O G:ASN358 3.7 36.9 1.0
O G:HOH813 3.8 30.5 1.0
CG2 D:THR40 3.9 36.0 1.0
ND2 G:ASN358 3.9 41.1 1.0
CA G:ASN358 4.3 34.0 1.0
O D:HOH675 4.4 25.9 1.0
CA D:THR40 4.4 30.4 1.0
N D:THR40 4.4 29.1 1.0
O G:HOH725 4.4 46.2 1.0
CA D:GLU39 4.4 33.0 1.0
C G:ASN358 4.4 33.5 1.0
O G:HOH638 4.5 42.9 1.0
OE1 D:GLU39 4.5 67.5 1.0
CB G:ASN358 4.5 34.5 1.0
CB D:THR40 4.7 32.2 1.0
CB D:GLU39 4.9 41.2 1.0

Sodium binding site 10 out of 13 in 8sf6

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Sodium binding site 10 out of 13 in the Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Promiscuous Amino Acid Gamma Synthase From Caldicellulosiruptor Hydrothermalis in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na504

b:51.4
occ:1.00
 O G:GLU39 2.3 36.3 1.0
O G:HOH830 2.3 43.4 1.0
OD1 D:ASN358 2.4 49.5 1.0
CG D:ASN358 3.3 47.0 1.0
C G:GLU39 3.5 36.6 1.0
O D:ASN358 3.6 39.4 1.0
ND2 D:ASN358 3.8 50.9 1.0
O D:HOH755 3.9 36.6 1.0
CG2 G:THR40 3.9 42.0 1.0
CA D:ASN358 4.3 42.4 1.0
N G:THR40 4.3 35.2 1.0
CA G:THR40 4.3 37.5 1.0
CA G:GLU39 4.4 37.7 1.0
CG G:GLU39 4.4 51.4 1.0
C D:ASN358 4.4 41.7 1.0
O G:HOH637 4.5 32.3 1.0
O D:HOH630 4.5 46.4 1.0
CB D:ASN358 4.5 44.7 1.0
CB G:THR40 4.7 39.7 1.0
CB G:GLU39 5.0 42.3 1.0

Reference:

A.Zmich, L.J.Perkins, C.Bingman, J.F.Acheson, A.R.Buller. Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in A Pyridoxal Phosphate-Dependent Protein Family. Acs Catalysis V. 13 11644 2023.
ISSN: ESSN 2155-5435
PubMed: 37720819
DOI: 10.1021/ACSCATAL.3C02498
Page generated: Wed Oct 9 13:27:22 2024

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