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Sodium in PDB 9f7m: Blastococcus Orn Bound to Pgg

Protein crystallography data

The structure of Blastococcus Orn Bound to Pgg, PDB code: 9f7m was solved by S.Mortensen, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.57, 117.701, 99.466, 90, 93.62, 90
R / Rfree (%) 17.1 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Blastococcus Orn Bound to Pgg (pdb code 9f7m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Blastococcus Orn Bound to Pgg, PDB code: 9f7m:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 9f7m

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Sodium binding site 1 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:25.8
occ:0.76
OD2 A:ASP165 2.3 41.9 1.0
OP1 I:G603 2.3 23.2 0.9
OE2 A:GLU14 2.3 36.5 1.0
O A:HOH498 2.4 37.9 1.0
O A:HOH546 3.1 37.3 1.0
OD2 A:ASP12 3.1 32.9 1.0
CG A:ASP165 3.2 38.7 1.0
OD1 A:ASP12 3.2 32.0 1.0
CD A:GLU14 3.4 32.0 1.0
CG A:ASP12 3.5 30.1 1.0
P I:G603 3.6 22.0 0.9
OE1 A:GLU14 3.7 26.1 1.0
CB A:ASP165 3.7 28.8 1.0
NA I:NA701 3.8 21.8 0.7
O A:HOH550 4.0 34.4 1.0
O A:HOH427 4.0 42.7 1.0
OD1 A:ASP165 4.2 43.5 1.0
O5' I:G603 4.2 23.9 1.0
O I:HOH805 4.3 43.7 1.0
OP2 I:G603 4.3 20.1 0.8
O A:HOH563 4.4 47.0 1.0
O A:HOH604 4.4 46.7 1.0
C5' I:G603 4.5 24.4 0.9
O A:CYS13 4.5 24.8 1.0
O I:HOH804 4.6 39.7 1.0
CG A:GLU14 4.7 28.6 1.0
O3' I:G602 4.7 23.0 0.9
O A:HOH452 4.8 26.9 1.0
CB A:ASP12 4.9 23.4 1.0

Sodium binding site 2 out of 10 in 9f7m

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Sodium binding site 2 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na701

b:21.8
occ:0.74
O A:HOH418 2.2 28.1 1.0
OD1 A:ASP12 2.3 32.0 1.0
O A:HOH550 2.4 34.4 1.0
O A:HOH452 2.4 26.9 1.0
OP1 I:G603 2.4 23.2 0.9
O3' I:G602 2.6 23.0 0.9
P I:G603 3.2 22.0 0.9
CG A:ASP12 3.6 30.1 1.0
NA A:NA301 3.8 25.8 0.8
C3' I:G602 3.9 21.8 1.0
O A:HOH518 3.9 25.9 1.0
O2' I:G602 3.9 21.1 0.8
O A:HOH492 4.1 30.3 1.0
OD2 A:ASP113 4.1 27.3 1.0
O A:HOH498 4.1 37.9 1.0
C5' I:G603 4.2 24.4 0.9
C4' I:G602 4.2 21.1 0.9
O5' I:G603 4.2 23.9 1.0
OD2 A:ASP12 4.3 32.9 1.0
OD1 A:ASP113 4.3 26.6 1.0
O A:CYS13 4.3 24.8 1.0
O A:ASN108 4.3 22.0 1.0
OP2 I:G603 4.4 20.1 0.8
C2' I:G602 4.5 19.1 1.0
CB A:ASP12 4.6 23.4 1.0
CG A:ASP113 4.6 26.9 1.0
O I:HOH802 4.8 27.4 1.0
C5' I:G602 4.8 21.3 1.0
N A:CYS13 4.8 23.3 1.0
CA A:ASP12 4.8 23.8 1.0

Sodium binding site 3 out of 10 in 9f7m

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Sodium binding site 3 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na701

b:24.5
occ:0.76
O B:HOH308 2.3 30.2 1.0
OD1 B:ASP12 2.3 28.1 1.0
O B:HOH463 2.4 35.6 1.0
O B:HOH398 2.4 26.2 1.0
OP1 J:G603 2.6 28.4 1.0
O3' J:G602 2.6 22.5 1.0
P J:G603 3.2 23.6 1.0
CG B:ASP12 3.5 27.9 1.0
C3' J:G602 3.8 22.6 1.0
O2' J:G602 3.8 22.9 1.0
OD2 B:ASP12 4.0 31.3 1.0
C4' J:G602 4.0 22.2 1.0
O J:HOH801 4.0 26.1 1.0
O B:HOH442 4.1 27.0 1.0
C5' J:G603 4.1 23.4 1.0
OD2 B:ASP113 4.2 29.4 1.0
O5' J:G603 4.2 25.1 1.0
O B:HOH372 4.2 29.2 1.0
OD1 B:ASP113 4.3 29.0 1.0
O B:ASN108 4.3 24.3 1.0
O B:CYS13 4.3 23.8 1.0
C2' J:G602 4.4 22.4 1.0
OP2 J:G603 4.5 24.8 1.0
CG B:ASP113 4.7 29.8 1.0
C5' J:G602 4.7 22.6 1.0
CB B:ASP12 4.7 24.6 1.0
O J:HOH803 4.8 31.7 1.0
N B:CYS13 4.8 24.7 1.0
CA B:ASP12 5.0 24.3 1.0

Sodium binding site 4 out of 10 in 9f7m

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Sodium binding site 4 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:27.8
occ:0.68
OP1 K:G603 2.3 25.7 1.0
OE2 C:GLU14 2.3 36.4 1.0
OD2 C:ASP165 2.5 44.6 1.0
OD2 C:ASP12 2.7 37.2 1.0
O C:HOH529 2.9 41.7 1.0
CG C:ASP165 3.3 39.2 1.0
OD1 C:ASP12 3.4 31.6 1.0
CD C:GLU14 3.4 33.0 1.0
CG C:ASP12 3.4 32.8 1.0
P K:G603 3.6 23.1 1.0
OE1 C:GLU14 3.7 27.5 1.0
CB C:ASP165 3.7 29.3 1.0
NA K:NA701 3.9 22.4 0.7
O5' K:G603 4.2 25.8 1.0
O C:HOH553 4.3 42.8 1.0
OD1 C:ASP165 4.3 40.3 1.0
O K:HOH809 4.3 36.0 1.0
OP2 K:G603 4.3 23.2 1.0
O C:CYS13 4.5 24.7 1.0
C5' K:G603 4.5 26.0 1.0
O K:HOH808 4.5 42.2 1.0
CG C:GLU14 4.7 27.7 1.0
O3' K:G602 4.7 23.1 1.0
CB C:ASP12 4.9 26.4 1.0
O C:HOH459 4.9 26.9 1.0
CA C:ALA162 5.0 30.2 1.0

Sodium binding site 5 out of 10 in 9f7m

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Sodium binding site 5 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na701

b:22.4
occ:0.70
OD1 C:ASP12 2.2 31.6 1.0
O C:HOH406 2.3 30.4 1.0
O C:HOH459 2.3 26.9 1.0
O K:HOH809 2.3 36.0 1.0
OP1 K:G603 2.5 25.7 1.0
O3' K:G602 2.6 23.1 1.0
P K:G603 3.1 23.1 1.0
CG C:ASP12 3.5 32.8 1.0
C3' K:G602 3.8 22.3 1.0
O C:HOH487 3.9 28.6 1.0
O2' K:G602 3.9 26.7 1.0
NA C:NA301 3.9 27.8 0.7
O C:HOH479 4.0 31.6 1.0
C4' K:G602 4.1 22.1 1.0
OD2 C:ASP113 4.1 28.5 1.0
OD2 C:ASP12 4.1 37.2 1.0
O5' K:G603 4.1 25.8 1.0
C5' K:G603 4.2 26.0 1.0
O C:ASN108 4.2 22.9 1.0
O C:CYS13 4.3 24.7 1.0
OP2 K:G603 4.3 23.2 1.0
OD1 C:ASP113 4.3 29.9 1.0
C2' K:G602 4.5 25.8 1.0
CB C:ASP12 4.6 26.4 1.0
O K:HOH802 4.6 29.3 1.0
CG C:ASP113 4.6 30.6 1.0
C5' K:G602 4.7 24.2 1.0
N C:CYS13 4.8 25.8 1.0
CA C:ASP12 4.8 24.3 1.0

Sodium binding site 6 out of 10 in 9f7m

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Sodium binding site 6 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na701

b:23.5
occ:0.70
O D:HOH1432 2.3 29.4 1.0
OD1 D:ASP12 2.3 26.1 1.0
O D:HOH1465 2.4 26.2 1.0
O L:HOH811 2.5 33.6 1.0
OP1 L:G603 2.5 28.3 1.0
O3' L:G602 2.5 25.3 1.0
P L:G603 3.1 24.5 1.0
CG D:ASP12 3.5 29.9 1.0
O2' L:G602 3.7 26.8 1.0
C3' L:G602 3.7 23.1 1.0
C4' L:G602 3.9 23.4 1.0
O D:HOH1530 4.0 26.1 1.0
OD2 D:ASP12 4.1 30.9 1.0
O D:HOH1487 4.1 27.8 1.0
C5' L:G603 4.1 24.1 1.0
O D:HOH1407 4.1 28.0 1.0
O5' L:G603 4.1 25.1 1.0
OD1 D:ASP113 4.1 27.4 1.0
O D:CYS13 4.2 26.1 1.0
OD2 D:ASP113 4.3 28.7 1.0
O D:ASN108 4.3 24.5 1.0
OP2 L:G603 4.3 24.0 1.0
C2' L:G602 4.4 22.9 1.0
C5' L:G602 4.6 22.1 1.0
CG D:ASP113 4.6 26.5 1.0
CB D:ASP12 4.7 23.5 1.0
O L:HOH804 4.7 26.1 1.0
N D:CYS13 4.7 26.6 1.0
CA D:ASP12 4.9 25.3 1.0

Sodium binding site 7 out of 10 in 9f7m

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Sodium binding site 7 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na701

b:23.4
occ:0.85
OD1 E:ASP12 2.3 24.7 1.0
O E:HOH321 2.4 27.7 1.0
O E:HOH367 2.4 23.7 1.0
O E:HOH466 2.5 31.2 1.0
OP1 M:G603 2.5 25.7 1.0
O3' M:G602 2.5 21.8 1.0
P M:G603 3.1 23.6 1.0
CG E:ASP12 3.5 25.7 1.0
O2' M:G602 3.7 25.3 1.0
C3' M:G602 3.7 19.6 1.0
C4' M:G602 4.0 21.1 1.0
O E:HOH304 4.0 25.2 1.0
OD2 E:ASP12 4.0 26.9 1.0
C5' M:G603 4.1 24.2 1.0
O5' M:G603 4.1 24.9 1.0
OD2 E:ASP113 4.1 27.4 1.0
O E:HOH435 4.1 27.0 1.0
O E:HOH365 4.2 27.3 1.0
O E:CYS13 4.2 24.1 1.0
OD1 E:ASP113 4.3 29.1 1.0
O E:ASN108 4.3 22.5 1.0
OP2 M:G603 4.3 23.5 1.0
C2' M:G602 4.4 23.0 1.0
CG E:ASP113 4.6 30.0 1.0
CB E:ASP12 4.7 21.6 1.0
C5' M:G602 4.7 24.2 1.0
N E:CYS13 4.8 20.9 1.0
O M:HOH802 4.9 29.0 1.0
CA E:ASP12 5.0 20.5 1.0

Sodium binding site 8 out of 10 in 9f7m

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Sodium binding site 8 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na701

b:23.7
occ:0.83
OD1 F:ASP12 2.3 30.2 1.0
O F:HOH319 2.3 25.5 1.0
O F:HOH358 2.4 25.6 1.0
O F:HOH378 2.4 31.5 1.0
OP1 N:G603 2.4 28.0 1.0
O3' N:G602 2.6 26.0 1.0
P N:G603 3.1 28.7 1.0
CG F:ASP12 3.5 32.5 1.0
C3' N:G602 3.8 24.6 1.0
O2' N:G602 3.8 27.1 1.0
O F:HOH311 4.0 34.9 1.0
O F:HOH330 4.0 38.8 1.0
C4' N:G602 4.0 22.6 1.0
O F:HOH347 4.0 29.8 1.0
OD2 F:ASP113 4.1 30.2 1.0
C5' N:G603 4.1 27.9 1.0
O5' N:G603 4.1 26.4 1.0
OD2 F:ASP12 4.2 35.4 1.0
O F:CYS13 4.2 26.6 1.0
OD1 F:ASP165 4.2 41.8 1.0
OP2 N:G603 4.3 28.5 1.0
OD1 F:ASP113 4.3 31.1 1.0
O F:ASN108 4.3 23.0 1.0
C2' N:G602 4.4 25.3 1.0
O F:HOH315 4.5 36.1 1.0
CB F:ASP12 4.6 25.0 1.0
CG F:ASP113 4.6 29.5 1.0
C5' N:G602 4.6 21.7 1.0
N F:CYS13 4.7 25.3 1.0
O N:HOH804 4.7 28.6 1.0
CA F:ASP12 4.8 25.4 1.0
CG F:ASP165 4.9 38.4 1.0
OD2 F:ASP165 4.9 38.3 1.0

Sodium binding site 9 out of 10 in 9f7m

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Sodium binding site 9 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na701

b:22.3
occ:0.75
OD1 G:ASP12 2.3 29.6 1.0
O G:HOH323 2.3 30.1 1.0
O G:HOH361 2.4 31.6 1.0
O G:HOH422 2.4 36.5 1.0
OP1 O:G603 2.5 27.6 1.0
O3' O:G602 2.6 26.2 1.0
P O:G603 3.2 26.7 1.0
CG G:ASP12 3.5 28.5 1.0
C3' O:G602 3.8 26.2 1.0
O2' O:G602 3.8 27.3 1.0
O O:HOH801 4.0 30.0 1.0
OD2 G:ASP12 4.0 33.9 1.0
C4' O:G602 4.0 22.9 1.0
O G:HOH367 4.1 28.9 1.0
C5' O:G603 4.1 30.5 1.0
O G:HOH411 4.1 28.5 1.0
OD1 G:ASP113 4.1 29.4 1.0
O5' O:G603 4.2 29.3 1.0
O G:CYS13 4.2 28.2 1.0
O G:ASN108 4.3 24.1 1.0
OD2 G:ASP113 4.3 30.4 1.0
OP2 O:G603 4.3 27.9 1.0
C2' O:G602 4.4 24.9 1.0
O O:HOH810 4.6 44.0 1.0
CB G:ASP12 4.6 24.9 1.0
CG G:ASP113 4.7 29.9 1.0
C5' O:G602 4.7 26.5 1.0
O O:HOH802 4.8 30.6 1.0
N G:CYS13 4.8 27.6 1.0
CA G:ASP12 5.0 27.8 1.0

Sodium binding site 10 out of 10 in 9f7m

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Sodium binding site 10 out of 10 in the Blastococcus Orn Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na701

b:29.4
occ:0.93
OD1 H:ASP12 2.2 33.6 1.0
O H:HOH358 2.4 32.9 1.0
O H:HOH311 2.5 34.8 1.0
OP1 P:G603 2.5 34.4 1.0
O3' P:G602 2.5 28.2 1.0
O H:HOH413 2.6 35.1 1.0
P P:G603 3.1 29.9 1.0
CG H:ASP12 3.4 32.8 1.0
C3' P:G602 3.8 29.3 1.0
O2' P:G602 3.8 29.2 1.0
OD2 H:ASP12 3.9 36.6 1.0
O H:HOH302 3.9 35.2 1.0
C4' P:G602 4.0 29.8 1.0
O H:HOH355 4.1 35.1 1.0
C5' P:G603 4.1 25.6 1.0
O H:CYS13 4.1 34.8 1.0
OD2 H:ASP113 4.1 36.7 1.0
O5' P:G603 4.1 28.0 1.0
O H:HOH392 4.2 31.4 1.0
OP2 P:G603 4.3 30.0 1.0
OD1 H:ASP113 4.4 34.4 1.0
O H:ASN108 4.4 25.9 1.0
C2' P:G602 4.4 27.6 1.0
CB H:ASP12 4.5 31.1 1.0
C5' P:G602 4.7 26.7 1.0
CG H:ASP113 4.7 33.0 1.0
N H:CYS13 4.7 30.7 1.0
CA H:ASP12 4.9 29.3 1.0
O P:HOH801 5.0 36.2 1.0

Reference:

S.Mortensen, H.Sondermann. Unique Dinucleases with Dna Specificity Are Associated with Genomic Islands in Actinomycetes and Clostridia To Be Published.
Page generated: Mon Aug 18 16:52:04 2025

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